Genetic loci associated with soybean cyst nematode resistance and methods of use

ABSTRACT

Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Divisional of U.S. application Ser. No.13/786,948, filed Mar. 6, 2013, which claims the benefit of U.S.Provisional Application No. 61/745,002, filed Dec. 21, 2012, which arehereby incorporated by reference in their entirety.

FIELD OF THE INVENTION

This invention relates to methods of identifying and/or selectingsoybean plants or germplasm that display improved resistance to SoybeanCyst Nematode.

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB

The official copy of the sequence listing is submitted concurrently withthe specification as a text file via EFS-Web, in compliance with theAmerican Standard Code for Information Interchange (ASCII), with a filename of 20160907_3208USDIV_SequenceListing.txt, a creation date of Sep.7, 2016 and a size of 111 KB. The sequence listing filed via EFS-Web ispart of the specification and is hereby incorporated in its entirety byreference herein.

BACKGROUND

Soybeans (Glycine max L. Merr.) are a major cash crop and investmentcommodity in North America and elsewhere. Soybean oil is one of the mostwidely used edible oils, and soybeans are used worldwide both in animalfeed and in human food production. Additionally, soybean utilization isexpanding to industrial, manufacturing, and pharmaceutical applications.

Soybean Cyst Nematode (SCN) is a parasitic pest which has threatenedsoybean production in the U.S. for more than fifty years. Soybean cystnematode resistance is an economically important trait as infection cansubstantially reduce yields. Molecular characterization of soybean cystnematode resistance would have important implications for soybeancultivar improvement.

There remains a need for soybean plants with improved resistance tosoybean cyst nematode and methods for identifying and selecting suchplants.

SUMMARY

Various methods and compositions are provided for identifying and/orselecting soybean plants or soybean germplasm with improved resistanceto soybean cyst nematode. In certain embodiments, the method comprisesdetecting at least one marker locus that is associated with resistanceto soybean cyst nematode. In other embodiments, the method furthercomprises detecting at least one marker profile or haplotype associatedwith resistance to soybean cyst nematode. In further embodiments, themethod comprises crossing a selected soybean plant with a second soybeanplant. Further provided are markers, primers, probes and kits useful foridentifying and/or selecting soybean plants or soybean germplasm withimproved resistance to soybean cyst nematode, as well as soybean plantsand seeds comprising one or more soybean cyst nematode loci.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 A-C provides a genetic map for loci on linkage group C1.

FIG. 2 A-B provides a genetic map for loci on linkage group B1.

FIG. 3 A-D provides a genetic map for loci on linkage group D2.

FIG. 4 A-D provide a genetic map for loci on LG B1. Genetic mappositions are based on the public integrated map (Hyten et al. (2010)Crop Sci 50:960-968). Physical map positions are based on the publicphysical map Glymal Williams 82 soybean reference assembly (Schmutz etal. (2010) Nature 463:178-183; and www.phytozome.net/soybean).

FIG. 5 A-C provides a genetic map for loci on linkage group D1b.

FIG. 6 A-C provides a genetic map for loci on linkage group C2.

FIG. 7 A-B provides a genetic map for loci on linkage group B2.

FIG. 8 A-B provides a genetic map for loci on linkage group E.

FIG. 9 A-B provides a genetic map for loci on linkage group L.

DETAILED DESCRIPTION

Before describing the present invention in detail, it is to beunderstood that this invention is not limited to particular embodiments,which can, of course, vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting.

Certain definitions used in the specification and claims are providedbelow. In order to provide a clear and consistent understanding of thespecification and claims, including the scope to be given such terms,the following definitions are provided:

As used in this specification and the appended claims, terms in thesingular and the singular forms “a,” “an,” and “the,” for example,include plural referents unless the content clearly dictates otherwise.Thus, for example, reference to “plant,” “the plant,” or “a plant” alsoincludes a plurality of plants; also, depending on the context, use ofthe term “plant” can also include genetically similar or identicalprogeny of that plant; use of the term “a nucleic acid” optionallyincludes, as a practical matter, many copies of that nucleic acidmolecule; similarly, the term “probe” optionally (and typically)encompasses many similar or identical probe molecules.

Additionally, as used herein, “comprising” is to be interpreted asspecifying the presence of the stated features, integers, steps, orcomponents as referred to, but does not preclude the presence oraddition of one or more features, integers, steps, or components, orgroups thereof. Thus, for example, a kit comprising one pair ofoligonucleotide primers may have two or more pairs of oligonucleotideprimers. Additionally, the term “comprising” is intended to includeexamples encompassed by the terms “consisting essentially of” and“consisting of.” Similarly, the term “consisting essentially of” isintended to include examples encompassed by the term “consisting of.”

“Agronomics,” “agronomic traits,” and “agronomic performance” refer tothe traits (and underlying genetic elements) of a given plant varietythat contribute to yield over the course of a growing season. Individualagronomic traits include emergence vigor, vegetative vigor, stressresistance, disease resistance or resistance, insect resistance orresistance, herbicide resistance, branching, flowering, seed set, seedsize, seed density, standability, threshability, and the like.

“Allele” means any of one or more alternative forms of a geneticsequence. In a diploid cell or organism, the two alleles of a givensequence typically occupy corresponding loci on a pair of homologouschromosomes. With regard to a SNP marker, allele refers to the specificnucleotide base present at that SNP locus in that individual plant.

The term “amplifying” in the context of nucleic acid amplification isany process whereby additional copies of a selected nucleic acid (or atranscribed form thereof) are produced. An “amplicon” is an amplifiednucleic acid, e.g., a nucleic acid that is produced by amplifying atemplate nucleic acid by any available amplification method

An “ancestral line” is a parent line used as a source of genes, e.g.,for the development of elite lines.

An “ancestral population” is a group of ancestors that have contributedthe bulk of the genetic variation that was used to develop elite lines.

“Backcrossing” is a process in which a breeder crosses a progeny varietyback to one of the parental genotypes one or more times.

The term “chromosome segment” designates a contiguous linear span ofgenomic DNA that resides in planta on a single chromosome. “Chromosomeinterval” refers to a chromosome segment defined by specific flankingmarker loci.

“Cultivar” and “variety” are used synonymously and mean a group ofplants within a species (e.g., Glycine max) that share certain genetictraits that separate them from other possible varieties within thatspecies. Soybean cultivars are inbred lines produced after severalgenerations of self-pollinations. Individuals within a soybean cultivarare homogeneous, nearly genetically identical, with most loci in thehomozygous state.

An “elite line” is an agronomically superior line that has resulted frommany cycles of breeding and selection for superior agronomicperformance. Numerous elite lines are available and known to those ofskill in the art of soybean breeding.

An “elite population” is an assortment of elite individuals or linesthat can be used to represent the state of the art in terms ofagronomically superior genotypes of a given crop species, such assoybean.

An “exotic soybean strain” or an “exotic soybean germplasm” is a strainor germplasm derived from a soybean not belonging to an available elitesoybean line or strain of germplasm. In the context of a cross betweentwo soybean plants or strains of germplasm, an exotic germplasm is notclosely related by descent to the elite germplasm with which it iscrossed. Most commonly, the exotic germplasm is not derived from anyknown elite line of soybean, but rather is selected to introduce novelgenetic elements (typically novel alleles) into a breeding program.

A “genetic map” is a description of genetic linkage relationships amongloci on one or more chromosomes (or linkage groups) within a givenspecies, generally depicted in a diagrammatic or tabular form.

“Genotype” is a description of the allelic state at one or more loci.

“Germplasm” means the genetic material that comprises the physicalfoundation of the hereditary qualities of an organism. As used herein,germplasm includes seeds and living tissue from which new plants may begrown; or, another plant part, such as leaf, stem, pollen, or cells,that may be cultured into a whole plant. Germplasm resources providesources of genetic traits used by plant breeders to improve commercialcultivars.

An individual is “homozygous” if the individual has only one type ofallele at a given locus (e.g., a diploid individual has a copy of thesame allele at a locus for each of two homologous chromosomes). Anindividual is “heterozygous” if more than one allele type is present ata given locus (e.g., a diploid individual with one copy each of twodifferent alleles). The term “homogeneity” indicates that members of agroup have the same genotype at one or more specific loci. In contrast,the term “heterogeneity” is used to indicate that individuals within thegroup differ in genotype at one or more specific loci.

“Introgression” means the entry or introduction of a gene, QTL,haplotype, marker profile, trait, or trait locus from the genome of oneplant into the genome of another plant.

The terms “label” or “detectable label” refer to a molecule capable ofdetection. A detectable label can also include a combination of areporter and a quencher, such as are employed in FRET probes or TaqMan™probes. The term “reporter” refers to a substance or a portion thereofwhich is capable of exhibiting a detectable signal, which signal can besuppressed by a quencher. The detectable signal of the reporter is,e.g., fluorescence in the detectable range. The term “quencher” refersto a substance or portion thereof which is capable of suppressing,reducing, inhibiting, etc., the detectable signal produced by thereporter. As used herein, the terms “quenching” and “fluorescence energytransfer” refer to the process whereby, when a reporter and a quencherare in close proximity, and the reporter is excited by an energy source,a substantial portion of the energy of the excited state non-radiativelytransfers to the quencher where it either dissipates non-radiatively oris emitted at a different emission wavelength than that of the reporter.

A “line” or “strain” is a group of individuals of identical parentagethat are generally inbred to some degree and that are generallyhomozygous and homogeneous at most loci (isogenic or near isogenic). A“subline” refers to an inbred subset of descendants that are geneticallydistinct from other similarly inbred subsets descended from the sameprogenitor. Traditionally, a subline has been derived by inbreeding theseed from an individual soybean plant selected at the F3 to F5generation until the residual segregating loci are “fixed” or homozygousacross most or all loci. Commercial soybean varieties (or lines) aretypically produced by aggregating (“bulking”) the self-pollinatedprogeny of a single F3 to F5 plant from a controlled cross between 2genetically different parents. While the variety typically appearsuniform, the self-pollinating variety derived from the selected planteventually (e.g., F8) becomes a mixture of homozygous plants that canvary in genotype at any locus that was heterozygous in the originallyselected F3 to F5 plant. Marker-based sublines that differ from eachother based on qualitative polymorphism at the DNA level at one or morespecific marker loci are derived by genotyping a sample of seed derivedfrom individual self-pollinated progeny derived from a selected F3-F5plant. The seed sample can be genotyped directly as seed, or as planttissue grown from such a seed sample. Optionally, seed sharing a commongenotype at the specified locus (or loci) are bulked providing a sublinethat is genetically homogenous at identified loci important for a traitof interest (e.g., yield, resistance, etc.).

“Linkage” refers to the tendency for alleles to segregate together moreoften than expected by chance if their transmission was independent.Typically, linkage refers to alleles on the same chromosome. Geneticrecombination occurs with an assumed random frequency over the entiregenome. Genetic maps are constructed by measuring the frequency ofrecombination between pairs of traits or markers, the lower thefrequency of recombination, and the greater the degree of linkage.

“Linkage disequilibrium” or “LD” is a non-random association of allelesat two or more loci and can occur between unlinked markers. It is basedon allele frequencies within a population and is influenced by but notdependent on linkage.

“Linkage group” (LG) refers to traits or markers that generallyco-segregate. A linkage group generally corresponds to a chromosomalregion containing genetic material that encodes the traits or markers.

“Locus” is a defined segment of DNA.

A “map location” or “map position” is an assigned location on a geneticmap relative to linked genetic markers where a specified marker can befound within a given species. Map positions are generally provided incentimorgans (cM), unless otherwise indicated, genetic positionsprovided are based on the Glycine max consensus map v 4.0 as provided byHyten et al. (2010) Crop Sci 50:960-968. A “physical position” or“physical location” or “physical map location” is the position,typically in nucleotides bases, of a particular nucleotide, such as aSNP nucleotide, on a chromosome. Unless otherwise indicated, thephysical position within the soybean genome provided is based on theGlyma 1.0 genome sequence described in Schmutz et al. (2010) Nature463:178-183, available from the Phytozome website(phytozome-dot-net/soybean).

“Mapping” is the process of defining the linkage relationships of locithrough the use of genetic markers, populations segregating for themarkers, and standard genetic principles of recombination frequency.

“Marker” or “molecular marker” or “marker locus” is a term used todenote a nucleic acid or amino acid sequence that is sufficiently uniqueto characterize a specific locus on the genome. Any detectablepolymorphic trait can be used as a marker so long as it is inheriteddifferentially and exhibits linkage disequilibrium with a phenotypictrait of interest.

“Marker assisted selection” refers to the process of selecting a desiredtrait or traits in a plant or plants by detecting one or more nucleicacids from the plant, where the nucleic acid is linked to the desiredtrait, and then selecting the plant or germplasm possessing those one ormore nucleic acids.

“Haplotype” refers to a combination of particular alleles present withina particular plant's genome at two or more linked marker loci, forinstance at two or more loci on a particular linkage group. Forinstance, in one example, two specific marker loci on LG-O are used todefine a haplotype for a particular plant. In still further examples, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or morelinked marker loci are used to define a haplotype for a particularplant.

As used herein, a “marker profile” means a combination of particularalleles present within a particular plant's genome at two or more markerloci which are not linked, for instance two or more loci on two or moredifferent linkage groups or two or more chromosomes. For instance, inone example, a particular combination of marker loci or a particularcombination of haplotypes define the marker profile of a particularplant.

The term “plant” includes reference to an immature or mature wholeplant, including a plant from which seed or grain or anthers have beenremoved. Seed or embryo that will produce the plant is also consideredto be the plant.

“Plant parts” means any portion or piece of a plant, including leaves,stems, buds, roots, root tips, anthers, seed, grain, embryo, pollen,ovules, flowers, cotyledons, hypocotyls, pods, flowers, shoots, stalks,tissues, tissue cultures, cells and the like.

“Polymorphism” means a change or difference between two related nucleicacids. A “nucleotide polymorphism” refers to a nucleotide that isdifferent in one sequence when compared to a related sequence when thetwo nucleic acids are aligned for maximal correspondence.

“Polynucleotide,” “polynucleotide sequence,” “nucleic acid,” “nucleicacid molecule,” “nucleic acid sequence,” “nucleic acid fragment,” and“oligonucleotide” are used interchangeably herein to indicate a polymerof nucleotides that is single- or multi-stranded, that optionallycontains synthetic, non-natural, or altered RNA or DNA nucleotide bases.A DNA polynucleotide may be comprised of one or more strands of cDNA,genomic DNA, synthetic DNA, or mixtures thereof.

“Primer” refers to an oligonucleotide which is capable of acting as apoint of initiation of nucleic acid synthesis or replication along acomplementary strand when placed under conditions in which synthesis ofa complementary strand is catalyzed by a polymerase. Typically, primersare about 10 to 30 nucleotides in length, but longer or shortersequences can be employed. Primers may be provided in double-strandedform, though the single-stranded form is more typically used. A primercan further contain a detectable label, for example a 5′ end label.

“Probe” refers to an oligonucleotide that is complementary (though notnecessarily fully complementary) to a polynucleotide of interest andforms a duplexed structure by hybridization with at least one strand ofthe polynucleotide of interest. Typically, probes are oligonucleotidesfrom 10 to 50 nucleotides in length, but longer or shorter sequences canbe employed. A probe can further contain a detectable label.

“Quantitative trait loci” or “QTL” refer to the genetic elementscontrolling a quantitative trait.

“Recombination frequency” is the frequency of a crossing over event(recombination) between two genetic loci. Recombination frequency can beobserved by following the segregation of markers and/or traits duringmeiosis.

“Resistance and “improved resistance” are used interchangeably hereinand refer to any type of increase in resistance or resistance to, or anytype of decrease in susceptibility. A “resistant plant” or “resistantplant variety” need not possess absolute or complete resistance.Instead, a “resistant plant,” “resistant plant variety,” or a plant orplant variety with “improved resistance” will have a level of resistanceor resistance which is higher than that of a comparable susceptibleplant or variety.

“Self-crossing” or “self-pollination” or “selfing” is a process throughwhich a breeder crosses a plant with itself; for example, a secondgeneration hybrid F2 with itself to yield progeny designated F2:3.

“SNP” or “single nucleotide polymorphism” means a sequence variationthat occurs when a single nucleotide (A, T, C, or G) in the genomesequence is altered or variable. “SNP markers” exist when SNPs aremapped to sites on the soybean genome.

The term “yield” refers to the productivity per unit area of aparticular plant product of commercial value. For example, yield ofsoybean is commonly measured in bushels of seed per acre or metric tonsof seed per hectare per season. Yield is affected by both genetic andenvironmental factors.

As used herein, an “isolated” or “purified” polynucleotide orpolypeptide, or biologically active portion thereof, is substantially oressentially free from components that normally accompany or interactwith the polynucleotide or polypeptide as found in its naturallyoccurring environment. Typically, an “isolated” polynucleotide is freeof sequences (optimally protein encoding sequences) that naturally flankthe polynucleotide (i.e., sequences located at the 5′ and 3′ ends of thepolynucleotide) in the genomic DNA of the organism from which thepolynucleotide is derived. For example, the isolated polynucleotide cancontain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kbof nucleotide sequence that naturally flank the polynucleotide ingenomic DNA of the cell from which the polynucleotide is derived. Apolypeptide that is substantially free of cellular material includespreparations of polypeptides having less than about 30%, 20%, 10%, 5%,or 1% (by dry weight) of contaminating protein, culture media or otherchemical components.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook, J.,Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual;Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989(hereinafter “Sambrook”).

Methods are provided for identifying and/or selecting a soybean plant orsoybean germplasm that displays improved resistance to soybean cystnematode. The method comprises detecting in the soybean plant orgermplasm, or a part thereof, at least one marker locus associated withresistance to soybean cyst nematode. Also provided are isolatedpolynucleotides and kits for use in identifying and/or detecting asoybean plant or soybean germplasm that displays improved resistance tosoybean cyst nematode, and soybean plants, cells, and/or seedscomprising at least one marker locus conferring improved resistance tosoybean cyst nematode, and soybean plants, cells, and/or seedscomprising at least one marker locus conferring improved resistance tosoybean cyst nematode.

Provided herein are marker loci associated with soybean cyst nematoderesistance that have been identified and mapped to genomic loci onlinkage groups D1b, B2, B1, C2, E, C1, D2, and L. These genomic regionsrepresent both major and minor QTLs associated with soybean cystnematode resistance.

These findings have important implications for soybean production, asidentifying markers that can be used for selection of soybean cystnematode resistance will greatly expedite the development of soybeancyst nematode resistance into elite cultivars.

Marker loci, haplotypes and marker profiles associated with resistanceto soybean cyst nematode, are provided. Further provided are genomicloci that are associated with soybean resistance to soybean cystnematode.

In certain embodiments, soybean plants or germplasm are identified thathave at least one favorable allele, marker locus, haplotype or markerprofile that positively correlates with resistance or improvedresistance to soybean cyst nematode. However, in other embodiments, itis useful for exclusionary purposes during breeding to identify alleles,marker loci, haplotypes, or marker profiles that negatively correlatewith resistance, for example, to eliminate such plants or germplasm fromsubsequent rounds of breeding.

In one embodiment, marker loci useful for identifying a first soybeanplant or first soybean germplasm that displays improved resistance tosoybean cyst nematode are between about marker Sat_123 and about markerSatt453 on linkage group B1. In a specific embodiment, the marker locuscomprises one or more of S04196-1-B, S04938-1-A, S04937-1-Q1,S08344-1-Q1, S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1,S04197-1 or a closely linked marker.

In another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode are between about marker Sat_207 andabout marker Satt713 on linkage group C1. In a specific embodiment, themarker locus comprises S07162-1-Q1, or a closely linked marker.

In yet another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode are between about marker Satt574 andabout marker Satt615 on linkage group D2. In a specific embodiment, themarker locus comprises S07161-1-Q1, or a closely linked marker.

Non-limiting examples of marker loci located within, linked to, orclosely linked to these genomic loci are provided in Table 1 and Table 9and FIGS. 1, 2, 3, 4, 5, 6, 7, 8 and 9.

TABLE 1 Marker Positions For Marker Loci Associated With Resistance toSoybean Cyst Nematode. Public Public Map Physical Marker FlankingPosition Map Physical Marker Linkage Public Region Position Map NameGroup Markers* (CM)* Region* Position** Allele (R/S) Source S04196-1-BB1 Sat_123- 100.87- 37220324- 37220579 *******/ Peking Satt453 123.9537220725 CATGCAA S04938-1-A B1 Sat_123- 100.87- 36954900- 36954994 C/TPeking Satt453 123.95 36955533 S04937-1-Q1 B1 Sat_123- 100.87- 36954339-36954799 T/C Peking Satt453 123.95 36954916 S08344-1-Q1 B1 Sat_123-100.87- 36781634- 36781754 C/T Peking Satt453 123.95 36781933S08343-1-Q1 B1 Sat_123- 100.87- 37020146- 37020399 C/A PI437654 Satt453123.95 37020659 S08346-1-Q1 B1 Sat_123- 100.87- 37020037- 37020092 CA .. . G/ PI437654 Satt453 123.95 37020146 GA . . . T S06786-1 B1 Sat_123-100.87- 37310886- 37311443 A/C Satt453 123.95 37311630 S06787-1 B1Sat_123- 100.87- 37333461- 37333894 G/T Satt453 123.95 37334083 S06803-1B1 Sat_123- 100.87- 37334355- 37334507 A/G Satt453 123.95 37335008S04197-1 B1 Sat_123- 100.87- 37117156- 37117244 C/A Peking Satt453123.95 37117406 S07162-1-Q1 C1 sat_207- 87.3- 42916694- 42916770 C/TPI437654 satt713 88.94 42916901 S07161-1-Q1 D2 satt574- 87.66- 34888639-34888681 A/T PI437654 satt615 91.2 34888798 *Gm composite v4.0 GeneticMap **JGI Glyma1 assembly

In certain embodiments, multiple marker loci that collectively make upthe soybean cyst nematode resistance haplotype of interest areinvestigated. For example, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of thevarious marker loci provided herein can comprise a soybean cyst nematoderesistance haplotype. In some embodiments, the haplotype comprises: (a)two or more marker loci found between about marker Sat_123 and aboutmarker Satt453 on linkage group B1; (b) two or more marker locicomprising S04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1,S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1 onlinkage group B1, or a closely linked marker; (c) two or more markerloci between about marker Sat_207 and about marker Satt713 on linkagegroup C1; and/or (d) two or more marker loci between about markerSatt574 and about marker Satt615 on linkage group D2.

In one embodiment, marker loci useful for identifying a first soybeanplant or first soybean germplasm that displays improved resistance tosoybean cyst nematode are in an interval flanked by and including markerlocus S00875 and about marker S02621 on linkage group D1b. In someexamples, the marker locus is in an interval flanked by and includingS00479 and S02136. In some examples, the marker is within 30 cM of oneor more of S00479, S02136, S00875, S12875, S12950, S12947, S12933,S12853, S03246, S01519, S12962, S00144, S08166, S08177, S01081, andS02621. In some examples, the marker is within 10 cM of one or more ofS00479, S02136, S00875, S12875, S12950, S12947, S12933, S12853, S03246,S01519, S12962, S00144, S08166, S08177, S01081, and S02621. In aspecific embodiment, the marker locus comprises one or more ofS01519-1-A; S08177-1-Q1; S00479-1-A; S02136-1-A; S00875-1-A;S12875-1-Q1; S12950-1-Q1; S12947-1-Q1; S12933-1-Q1; S12853-1-Q1;S03246-1-A or S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, andS02621-1-A, or a marker closely linked thereto.

In another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode are in an interval flanked by andincluding Sat_264 and about BARC-020449-04623 on linkage group B2. Insome examples one or more loci are in an interval flanked by andincluding S02874 and S04785- on linkage group B2. In some examples, themarker is within 30 cM of one or more of S02864 and S04785. In someexamples, the marker is within 10 cM of one or more of S02864 andS04785. In a specific embodiment, the marker locus comprises S02874-1-A,S04785-1-A, or a marker closely linked thereto.

In yet another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode in an interval flanked by andincluding S04348 and S01999 on linkage group B1. In some examples, themarker is within 30 cM of one or more of S04348, S01209, or S01999. Insome examples, the marker is within 10 cM of one or more of S04348,S01209, or S01999. In a specific embodiment, the marker locus comprisesS04348-1-A, S01209-1-A, S01999-1-A, or a marker closely linked thereto.

In another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode in an interval flanked by andincluding S01209 and S01999 on linkage group B1.

In another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode associated with one or more markerlocus selected from the group consisting of S04937-2-A, S04937-1-Q1,S04938-1-A, S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1,S06787-2-Q1, S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1,S06805-1-Q1, S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1,S06792-1-Q1.

In another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst in an interval flanked by and includingSatt557 and Satt307 on linkage group C2. In some examples the intervalis flanked by and includes S03252 and S02112 on linkage group C2. Insome examples, the marker is within 30 cM of one or more of S03252 orS02112. In some examples, the marker is within 10 cM of one or more ofS03252 or S02112. In a specific embodiment, the marker locus comprisesS03252-1-A, S02112-1-A, or a marker closely linked thereto.

In another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode in an interval comprising the bottom30 cM of linkage group E, for example from about 66 cM to the end. Insome example the interval is flanked by and includes BARC-062799-18070to the end of linkage group E. In some examples the interval is flankedby and includes Sat_107 to the end of linkage group E. In some examplesthe interval is flanked by and includes S00350 to S02183 on linkagegroup E. In some examples, the marker is within 30 cM of one or more ofS00350 or S02183. In some examples, the marker is within 10 cM of one ormore of S00350 or S02183. In a specific embodiment, the marker locuscomprises S00350-1-A, S02183-1-A, or a marker closely linked thereto.

In another embodiment, marker loci useful for identifying a firstsoybean plant or first soybean germplasm that displays improvedresistance to soybean cyst nematode in an interval comprising the top 30cM of linkage group L, for example from about 0-30 cM. In some examplesthe interval is flanked by and comprises S02074 and S03991 on linkagegroup L. In some examples, the marker is within 30 cM of one or more ofS02074 or S03991. In some examples, the marker is within 10 cM of one ormore of S02074 or S03991. In a specific embodiment, the marker locuscomprises S02074-1-A, S03991-1-A, or a marker closely linked thereto.

Non-limiting examples of marker loci located within, linked to, orclosely linked to these genomic loci are provided in Table 1 and 9 andFIGS. 1, 2, 3, 4, 5, 6, 7, 8 and 9.

In certain embodiments, multiple marker loci that collectively make upthe soybean cyst nematode resistance haplotype of interest areinvestigated. For example, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of thevarious marker loci provided herein can comprise a soybean cyst nematoderesistance haplotype. In some embodiments, the haplotype comprises: (a)two or more marker locus flanked by and including S04348 and S01999 onlinkage group B1; (b) two or more marker locus within 30 cM of one ormore of S04348, S01209, or S01999 on linkage group B1; (c) two or moremarker locus within 10 cM of one or more of S04348, S01209, or S01999 onlinkage group B1; (d) two or more marker locus comprising S04348-1-A,S01209-1-A, S01999-1-A, or a marker closely linked thereto on linkagegroup B1; (e) two or more marker locus flanked by and including S01209and S01999 on linkage group B1; (f) two or more marker locus selectedfrom the group consisting of S04937-2-A, S04937-1-Q1, S04938-1-A,S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1, S06787-2-Q1,S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1, S06805-1-Q1,S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, or S06792-1-Q1 onlinkage group B1; (g) two or more marker locus flanked by Satt557 andSatt307 on linkage group C2; (h) two or more marker locus flanked byS03252 and S02112 on linkage group C2; (i) two or more marker locuswithin 30 cM of one or more of S03252 or S02112 on linkage group C2; (j)two or more marker locus within 10 cM of one or more of S03252 or S02112on linkage group C2; (k) two or more marker locus comprising S03252-1-A,S02112-1-A, or a marker closely linked thereto on linkage group C2; (1)two or more marker locus an interval comprising the bottom 30 cM oflinkage group E, for example from about 66 cM to the end; (m) two ormore marker locus flanked by BARC-062799-18070 to the end of linkagegroup E; (n) two or more marker locus flanked by Sat_107 to the end oflinkage group E; (o) two or more marker locus flanked by S00350 toS02183 on linkage group E; (p) two or more marker locus within 30 cM ofone or more of S00350 or S02183 on linkage group E; (q) two or moremarker locus within 10 cM of one or more of S00350 or S02183 on linkagegroup E; (r) two or more marker locus comprising S00350-1-A, S02183-1-A,or a marker closely linked thereto on linkage group E; (s) two or moremarker locus in an interval comprising the top 30 cM of linkage group L,for example from about 0-30 cM; (t) two or more marker locus in aninterval is flanked by S02074 and S03991 on linkage group L; (u) two ormore marker locus within 30 cM of one or more of S02074 or S03991 onlinkage group L; (v) two or more marker locus within 10 cM of one ormore of S02074 or S03991 on linkage group L; (w) two or more markerlocus comprising S02074-1-A, S03991-1-A, or a marker closely linkedthereto on linkage group L; (x) two or more marker locus flanked bymarker locus S00875 and about marker S02621 on linkage group D1b; (y)two or more marker locus flanked by S00479 and S02136 on linkage groupD1b; (z) two or more maker locus within 30 cM of one or more of S00479,S02136, S00875, S12875, S12950, S12947, S12933, S12853, S03246, S01519,S12962, S00144, S08166, S08177, S01081, and S02621 on linkage group D1b;(aa) two or more marker locus within 10 cM of one or more of S00479,S02136, S00875, S12875, S12950, S12947, S12933, S12853, S03246, S01519,S12962, S00144, S08166, S08177, S01081, and S02621 on linkage group D1b;(ab) two or more marker locus comprising one or more of S01519-1-A;S08177-1-Q1; S00479-1-A; S02136-1-A; S00875-1-A; S12875-1-Q1;S12950-1-Q1; S12947-1-Q1; S12933-1-Q1; S12853-1-Q1; S03246-1-A orS12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, and S02621-1-A, or a markerclosely linked thereto on linkage group D1b; (ac) two or more markerlocus flanked by Sat_264 and about BARC-020449-04623 on linkage groupB2; (ad) two or more marker locus flanked by S02874 and S04785 onlinkage group B2; (ae) two or more marker locus within 30 cM of one ormore of S02864 and S04785 on linkage group B2; (af) two or more markerlocus within 10 cM of one or more of S02864 and S04785 on linkage groupB2; and/or (ag) two or more marker locus comprises S02874-1-A,S04785-1-A, or a marker closely linked thereto on linkage group B2.

In one embodiment, the method of identifying a first soybean plant or afirst soybean germplasm that displays improved resistance to soybeancyst nematode comprises detecting in the genome of the first soybeanplant or in the genome of the first soybean germplasm at least onehaplotype that is associated with the resistance, wherein the at leastone haplotype comprises at least two of the various marker loci providedherein.

In certain embodiments, two or more marker loci or haplotypes cancollectively make up a marker profile. The marker profile can compriseany two or more marker loci comprising: (a) any marker loci betweenabout marker Sat_123 and about marker Satt453 on linkage group B1; (b)marker loci comprising S04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1,S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1 onlinkage group B1, or a closely linked marker; (c) any marker locibetween about marker Sat_207 and about marker Satt713 on linkage groupC1; (d) marker loci comprising S07162-1-Q1 on linkage group C1, or aclosely linked marker; (e) any marker loci between about marker Satt574and about marker Satt615 on linkage group D2; and/or (f) marker locicomprising S07161-1-Q1 on linkage group D2, or a closely linked marker;(g) marker loci comprising S07160-1 on linkage group A2, or a closelylinked marker; (h) any marker loci associated with the rhg4 locus onlinkage group A2; (i) any marker loci associated with the rhg1 locus onlinkage group G, or a closely linked marker; (j) any marker lociassociated with the rhg2 locus on linkage group M; and/or (k) any markerloci associated with resistance to soybean cyst nematode.

In certain embodiments, two or more marker loci or haplotypes cancollectively make up a marker profile. The marker profile can compriseany two or more marker loci comprising: (a) two or more marker locusflanked by and including S04348 and S01999 on linkage group B1; (b) twoor more marker locus within 30 cM of one or more of S04348, S01209, orS01999 on linkage group B1; (c) two or more marker locus within 10 cM ofone or more of S04348, S01209, or S01999 on linkage group B1; (d) two ormore marker locus comprising S04348-1-A, S01209-1-A, S01999-1-A, or amarker closely linked thereto on linkage group B1; (e) two or moremarker locus flanked by and including S01209 and S01999 on linkage groupB1; (f) two or more marker locus selected from the group consisting ofS04937-2-A, S04937-1-Q1, S04938-1-A, S04938-2-A, S06786-2-Q1,S06786-3-Q1, S06786-1-Q1, S06787-2-Q1, S06787-1-Q1, S06803-1-Q1,S06804-1-Q1, S06788-1-Q1, S06805-1-Q1, S06789-1-Q1, S06790-1-Q1,S06791-2-Q1, S06791-1-Q1, or S06792-1-Q1 on linkage group B1; (g) two ormore marker locus flanked by Satt557 and Satt307 on linkage group C2;(h) two or more marker locus flanked by S03252 and S02112 on linkagegroup C2; (i) two or more marker locus within 30 cM of one or more ofS03252 or S02112 on linkage group C2; (j) two or more marker locuswithin 10 cM of one or more of S03252 or S02112 on linkage group C2; (k)two or more marker locus comprising S03252-1-A, S02112-1-A, or a markerclosely linked thereto on linkage group C2; (1) two or more marker locusan interval comprising the bottom 30 cM of linkage group E, for examplefrom about 66 cM to the end; (m) two or more marker locus flanked byBARC-062799-18070 to the end of linkage group E; (n) two or more markerlocus flanked by Sat_107 to the end of linkage group E; (o) two or moremarker locus flanked by S00350 to S02183 on linkage group E; (p) two ormore marker locus within 30 cM of one or more of S00350 or S02183 onlinkage group E; (q) two or more marker locus within 10 cM of one ormore of S00350 or S02183 on linkage group E; (r) two or more markerlocus comprising S00350-1-A, S02183-1-A, or a marker closely linkedthereto on linkage group E; (s) two or more marker locus in an intervalcomprising the top 30 cM of linkage group L, for example from about 0-30cM; (t) two or more marker locus in an interval is flanked by S02074 andS03991 on linkage group L; (u) two or more marker locus within 30 cM ofone or more of S02074 or S03991 on linkage group L; (v) two or moremarker locus within 10 cM of one or more of S02074 or S03991 on linkagegroup L; (w) two or more marker locus comprising S02074-1-A, S03991-1-A,or a marker closely linked thereto on linkage group L; (x) two or moremarker locus flanked by marker locus S00875 and about marker S02621 onlinkage group D1b; (y) two or more marker locus flanked by S00479 andS02136 on linkage group D1b; (z) two or more maker locus within 30 cM ofone or more of S00479, S02136, S00875, S12875, S12950, S12947, S12933,S12853, S03246, S01519, S12962, S00144, S08166, S08177, S01081, andS02621 on linkage group D1b; (aa) two or more marker locus within 10 cMof one or more of S00479, S02136, S00875, S12875, S12950, S12947,S12933, S12853, S03246, S01519, S12962, S00144, S08166, S08177, S01081,and S02621 on linkage group D1b; (ab) two or more marker locuscomprising one or more of S01519-1-A; S08177-1-Q1; S00479-1-A;S02136-1-A; S00875-1-A; S12875-1-Q1; S12950-1-Q1; S12947-1-Q1;S12933-1-Q1; S12853-1-Q1; S03246-1-A or S12962-1-Q1 S00144-1-A,S08166-1-Q1, S01081, and S02621-1-A, or a marker closely linked theretoon linkage group D1b; (ac) two or more marker locus flanked by Sat_264and about BARC-020449-04623 on linkage group B2; (ad) two or more markerlocus flanked by S02874 and S04785 on linkage group B2; (ae) two or moremarker locus within 30 cM of one or more of S02864 and S04785 on linkagegroup B2; (af) two or more marker locus within 10 cM of one or more ofS02864 and S04785 on linkage group B2; and/or (ag) two or more markerlocus comprises S02874-1-A, S04785-1-A, or a marker closely linkedthereto on linkage group B2; (ah) marker loci comprising S07160-1 onlinkage group A2, or a closely linked marker; (ai) any marker lociassociated with the rhg4 locus on linkage group A2; (aj) any marker lociassociated with the rhg1 locus on linkage group G, or a closely linkedmarker; (ak) any marker loci associated with the rhg2 locus on linkagegroup M; and/or (al) any marker loci associated with resistance tosoybean cyst nematode.

Any of the marker loci in any of the genomic loci disclosed herein canbe combined in the marker profile. For example, the marker profile cancomprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, or more marker loci or haplotypes associated with resistance tosoybean cyst nematode provided herein.

In one embodiment, a method of identifying a first soybean plant or afirst soybean germplasm that displays improved resistance to soybeancyst nematode comprises detecting in the genome of the first soybeanplant or in the genome of the first soybean germplasm at least onemarker profile that is associated with the resistance, wherein the atleast one marker profile comprises at least two of the various markerloci provided herein.

Not only can one detect the various markers provided herein, it isrecognized that one could detect any markers that are closely linked tothe various markers discussed herein.

In addition to the markers discussed herein, information regardinguseful soybean markers can be found, for example, on the USDA's Soybasewebsite, available at www.soybase.org. One of skill in the art willrecognize that the identification of favorable marker alleles may begermplasm-specific. The determination of which marker alleles correlatewith resistance (or susceptibility) is determined for the particulargermplasm under study. One of skill will also recognize that methods foridentifying the favorable alleles are routine and well known in the art,and furthermore, that the identification and use of such favorablealleles is well within the scope of the invention.

Various methods are provided to identify soybean plants and/or germplasmwith improved resistance to soybean cyst nematode. In one embodiment,the method of identifying comprises detecting at least one marker locusassociated with resistance to soybean cyst nematode. The term“associated with” in connection with a relationship between a markerlocus and a phenotype refers to a statistically significant dependenceof marker frequency with respect to a quantitative scale or qualitativegradation of the phenotype. Thus, an allele of a marker is associatedwith a trait of interest when the allele of the marker locus and thetrait phenotypes are found together in the progeny of an organism moreoften than if the marker genotypes and trait phenotypes segregatedseparately.

Any combination of the marker loci provided herein can be used in themethods to identify a soybean plant or soybean germplasm that displaysimproved resistance to soybean cyst nematode. Any one marker locus orany combination of the markers set forth in Table 1 and 9 or FIG. 1, 2,3, 4, 5, 6, 7, 8 or 9, or any closely linked marker can be used to aidin identifying and selecting soybean plants or soybean germplasm withimproved resistance to soybean cyst nematode.

In one embodiment, a method of identifying a first soybean plant or afirst soybean germplasm that displays improved resistance to soybeancyst nematode is provided. The method comprises detecting in the genomeof the first soybean plant or first soybean germplasm an allele of atleast one marker locus that is associated with resistance. In such amethod, the at least one marker locus: (A) can be between about markerSat_123 and about marker Satt453 on linkage group B1; (B) can compriseone or more of the marker loci S04196-1-B, S04938-1-A, S04937-1-Q1,S08344-1-Q1, S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1,S04197-1 on linkage group B1, or a closely linked marker; (C) can bebetween about marker Sat_207 and about marker Satt713 on linkage groupC1; (D) can comprise the marker locus S07162-1-Q1, or a closely linkedmarker; (E) can be between about marker Satt574 and about marker Satt615on linkage group D2; and/or (F) can comprise the marker locusS07161-1-Q1, or a closely linked marker.

In one embodiment, a method of identifying a first soybean plant or afirst soybean germplasm that displays improved resistance to soybeancyst nematode is provided. The method comprises detecting in the genomeof the first soybean plant or first soybean germplasm at least onemarker locus that is associated with resistance. In such a method, theat least one marker locus (a) is flanked by S04348 and S01999 on linkagegroup B1; (b) two or more marker locus within 30 cM of one or more ofS04348, S01209, or S01999 on linkage group B1; (c) is within 10 cM ofone or more of S04348, S01209, or S01999 on linkage group B1; (d)comprises S04348-1-A, S01209-1-A, S01999-1-A, or a marker closely linkedthereto on linkage group B1; (e) is flanked by S01209 and S01999 onlinkage group B1; (f) is selected from the group consisting ofS04937-2-A, S04937-1-Q1, S04938-1-A, S04938-2-A, S06786-2-Q1,S06786-3-Q1, S06786-1-Q1, S06787-2-Q1, S06787-1-Q1, S06803-1-Q1,S06804-1-Q1, S06788-1-Q1, S06805-1-Q1, S06789-1-Q1, S06790-1-Q1,S06791-2-Q1, S06791-1-Q1, or S06792-1-Q1 or a marker closely linkedthereto on linkage group B1; (g) is flanked by Satt557 and Satt307 onlinkage group C2; (h) is flanked by S03252 and S02112 on linkage groupC2; (i) is within 30 cM of one or more of S03252 or S02112 on linkagegroup C2; (j) is within 10 cM of one or more of S03252 or S02112 onlinkage group C2; (k) comprises S03252-1-A, S02112-1-A, or a markerclosely linked thereto on linkage group C2; (1) is in an intervalcomprising the bottom 30 cM of linkage group E, for example from about66 cM to the end; (m) is flanked by BARC-062799-18070 to the end oflinkage group E; (n) is flanked by Sat_107 to the end of linkage groupE; (o) is flanked by S00350 to S02183 on linkage group E; (p) is within30 cM of one or more of S00350 or S02183 on linkage group E; (q) iswithin 10 cM of one or more of S00350 or S02183 on linkage group E; (r)comprises S00350-1-A, S02183-1-A, or a marker closely linked thereto onlinkage group E; (s) is in an interval comprising the top 30 cM oflinkage group L, for example from about 0-30 cM; (t) is in an intervalis flanked by S02074 and S03991 on linkage group L; (u) is within 30 cMof one or more of S02074 or S03991 on linkage group L; (v) is within 10cM of one or more of S02074 or S03991 on linkage group L; (w) comprisesS02074-1-A, S03991-1-A, or a marker closely linked thereto on linkagegroup L; (x) is flanked by marker locus S00875 and about marker S02621on linkage group D1b; (y) is flanked by S00479 and S02136 on linkagegroup D1b; (z) is within 30 cM of one or more of S00479, S02136, S00875,S12875, S12950, S12947, S12933, S12853, S03246, S01519, S12962, S00144,S08166, S08177, S01081, and S02621 on linkage group D1b; (aa) is within10 cM of one or more of S00479, S02136, S00875, S12875, S12950, S12947,S12933, S12853, S03246, S01519, S12962, S00144, S08166, S08177, S01081,and S02621 on linkage group D1b; (ab) comprises one or more ofS01519-1-A; S08177-1-Q1; S00479-1-A; S02136-1-A; S00875-1-A;S12875-1-Q1; S12950-1-Q1; S12947-1-Q1; S12933-1-Q1; S12853-1-Q1;S03246-1-A or S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, andS02621-1-A, or a marker closely linked thereto on linkage group D1b;(ac) is flanked by Sat_264 and about BARC-020449-04623 on linkage groupB2; (ad) is flanked by S02874 and S04785 on linkage group B2; (ae) iswithin 30 cM of one or more of S02864 and S04785 on linkage group B2;(af) is within 10 cM of one or more of S02864 and S04785 on linkagegroup B2; and/or (ag) comprises S02874-1-A, S04785-1-A, or a markerclosely linked thereto on linkage group B2.

In other embodiments, two or more marker loci are detected in themethod. In a specific embodiment, the germplasm is a soybean variety.

In other embodiments, the method further comprises crossing the selectedfirst soybean plant or first soybean germplasm with a second soybeanplant or second soybean germplasm. In a further embodiment of themethod, the second soybean plant or second soybean germplasm comprisesan exotic soybean strain or an elite soybean strain.

In specific embodiments, the first soybean plant or first soybeangermplasm comprises a soybean variety. Any soybean line known to the artor disclosed herein may be used. Non-limiting examples of soybeanvarieties and their associated soybean cyst nematode resistance allelesencompassed by the methods provided herein include, for example, thoselisted in Table 1 and 9 and FIGS. 1, 2, 3, 4, 5, 6, 7, 8 and 9.

In another embodiment, the detection method comprises amplifying atleast one marker locus and detecting the resulting amplified markeramplicon. In such a method, amplifying comprises (a) admixing anamplification primer or amplification primer pair for each marker locusbeing amplified with a nucleic acid isolated from the first soybeanplant or the first soybean germplasm such that the primer or primer pairis complementary or partially complementary to a variant or fragment ofthe genomic locus comprising the marker locus and is capable ofinitiating DNA polymerization by a DNA polymerase using the soybeannucleic acid as a template; and (b) extending the primer or primer pairin a DNA polymerization reaction comprising a DNA polymerase and atemplate nucleic acid to generate at least one amplicon. In such amethod, the primer or primer pair can comprise a variant or fragment ofone or more of the genomic loci provided herein.

In one embodiment, the method involves amplifying a variant or fragmentof one or more polynucleotides comprising SEQ ID NOS: 135, 136, 137,138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151,152, 153, 154, 155, 156, 157, 158, 339, 340, 341, 342, 343, 344, 345,346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359,360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373,374, 375, 376, and/or 377 or variants or fragments thereof. In oneembodiment, the primer or primer pair can comprise a variant or fragmentof one or more polynucleotides comprising SEQ ID NOS: 135, 136, 137,138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151,152, 153, 154, 155, 156, 157, 158, 339, 340, 341, 342, 343, 344, 345,346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359,360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373,374, 375, 376, and/or 377 or complements thereof. In specificembodiments, the primer or primer pair comprises a nucleic acid sequencecomprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186,187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200,201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214,215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228,229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242,243, 244, 245, 246, 247, and/or 248 or variants or fragments thereof.

In a specific embodiment, the primer pair comprises SEQ ID NO:1 and SEQID NO:2, SEQ ID NO: 8 and SEQ ID NO:9, SEQ ID NO: 10 and SEQ ID NO:13,SEQ ID NO: 18 and SEQ ID NO:19, SEQ ID NO: 31 and SEQ ID NO:32, SEQ IDNO: 39 and SEQ ID NO:40, SEQ ID NO: 50 and SEQ ID NO:51, SEQ ID NO: 64and SEQ ID NO:65, SEQ ID NO: 66 and SEQ ID NO:67, SEQ ID NO: 72 and SEQID NO:73, or SEQ ID NO: 82 and SEQ ID NO:83 or the primer pairs setforth in Table 3.

In another embodiment, the method further comprises providing one ormore labeled nucleic acid probes suitable for detection of each markerlocus being amplified. In such a method, the labeled nucleic acid probecan comprise a sequence comprising a variant or fragment of one or moreof the genomic loci provided herein. In one embodiment, the labelednucleic acid probe can comprise a sequence comprising a variant orfragment of one or more polynucleotides comprising SEQ ID NOS: 135, 136,137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150,151, 152, 153, 154, 155, 156, 157, 158, 339, 340, 341, 342, 343, 344,345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358,359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372,373, 374, 375, 376, and/or 377 or complements thereof. In specificembodiments, the labeled nucleic acid probe comprises a nucleic acidsequence comprising SEQ ID NOS: 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 249,250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263,264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277,278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305,306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319,320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333,334, 335, 336, 337, and/or 338 or variants or fragments thereof.

Non-limiting examples of primers, probes, genomic loci and ampliconsthat can be used in the methods and compositions provided herein aresummarized in Tables 2, 3, 4, 5, 6, 7, and 8.

TABLE 2 Non-Limiting Examples of Primer Sequences. Linkage SEQ MarkerGroup Primer ID Allele position (ch) Locus Name NO Primer Sequence(Res/Sus) 37220579 B1 S04196-1 141527  1 GCCATCCTAGCTAGC *******/ (Gm11)CCTGT CATGCAA 37220579 B1 S04196-1 141528  2 TTGACCTGTTGATTA *******/(Gm11) TTTCGTAATG CATGCAA 37220579 B1 S04196-1 S4196-F2  3GCCATCCTAGCTAGC *******/ (Gm11) CCTGTATAT CATGCAA 37220579 B1 S04196-1S4196-R2  4 GTGTTAGGTGTCATC *******/ (Gm11) GAGGCAT CATGCAA 37220579 B1S04196-1 S4196-F3  5 TCCTAGCTAGCCCTG *******/ (Gm11) TATATTTTGA CATGCAA37220579 B1 S04196-1 S4196-R3  6 TAGGTGTCATCGAGG *******/ (Gm11) CATCGCATGCAA 37220579 B1 S04196-1 S4196-R4  7 AATTATCTTGACCTG *******/ (Gm11)TTGATTATTTCG CATGCAA 36954994 B1 S04938-1 S04938-  8 CCACAACCTATTGTT C/T(Gm11) F1 GAAGCAC 36954994 B1 S04938-1 S04938-  9 TGTGCACTCCTGACT C/T(Gm11) R1 GCTTT 36954799 B1 S04937-1 141535, 10 TCAACCGTGGAAAGT T/C(Gm11) S04937- AACCA F1 36954799 B1 S04937-1 141536 11 GTTCTTGAAAGTTGGT/C (Gm11) AGACTRAATG 36954799 B1 S04937-1 148638, 12 TCCTTGGAAGGTTCGT/C (Gm11) S04937- GTAGA F5 36954799 B1 S04937-1 148639, 13TCAATTTAGTTCTTG T/C S04937- AAAGTTGGAGAC R3 36954799 B1 S04937-1 S04937-14 AACCGTGGAAAGTAA T/C (Gm11) F3 CCAAAAA 36954799 B1 S04937-1 S04937- 15ACCTCAACCGTGGAA T/C (Gm11) F4 AGTAACC 36954799 B1 S04937-1 S04937- 16GGAATGACATTAACT T/C (Gm11) R4 TGGTTTTTGA 36954799 B1 S04937-1 S04937- 17TGACATTAACTTGGT T/C (Gm11) R5 TTTTGATCCT 36781754 B1 S08344-1 136830 18CGACACCAATTTCTC C/T (Gm11) CATCC 36781754 B1 S08344-1 136831 19ATGTCGGAACTTGGC C/T (Gm11) ATCTT 36781754 B1 S08344-1 P12198A1- 20CACGACACCAATTTC C/T (Gm11) F(128-) TCCATCCTCTCA 76806 86074: 36781754 B1S08344-1 P12198A- 21 CAACATTCCCAGTCG C/T (Gm11) 1T66A21 ACACGTCTTCT 8F86075: 36781754 B1 S08344-1 P12198A- 22 AAGGCATGTCGGAAC C/T (Gm11)1T66A21 TTGGCATCT 8R 36781754 B1 S08344-1 92472- 23 TGATTTCCAATGTAA C/T(Gm11) p12198A1_R ATCAACCATT 36781754 B1 S08344-1 136828 24AATACCCTTCCACGA C/T (Gm11) CACCA 36781754 B1 S08344-1 136829 25CGGAACTTGGCATCT C/T (Gm11) TTGAT 36781754 B1 S08344-1 136832 25TCAAACTTGACAAAG C/T (Gm11) CCACAA 36781754 B1 S08344-1 136833 27TGCAAAGAGGGTAAG C/T (Gm11) GACTTG 37020399 B1 S08343-1 19661 28CCATTTTTGGAGAAT C/A (Gm11) CTCGTGTCCGTAG 37020399 B1 S08343-1 19389 29GACTTACCAAATGAG C/A (Gm11) TTTGACCAGGTTTTA CC 37020399 B1 S08343-1 9634730 GATGATYCCAAATCT C/A (Gm11) GCTTCA 37020092 B1 S08346-1 136886 31TTGTTCTCCCGYTTA CA.... (Gm11) CACCA G/GA....T 37020092 B1 S08346-1136887 32 TGATACAACGYCCCA CA.... (Gm11) TTCTTC G/GA....T 37020092 B1S08346-1 P8584A- 33 GGTCAAACTCATTTG CA.... (Gm11) 1-F2, GTAAGTCTRAGTTTGG/GA....T 82593 C 37020092 B1 S08346-1 Reverse 34 CCCATTCTTCATGTA CA....(Gm11) primer CTCATACACCAAGAG G/GA....T 15081 37020092 B1 S08346-1136884 35 TTCTCCCGYTTACAC CA.... (Gm11) CACAA G/GA....T 37020092 B1S08346-1 136885 36 CAACGYCCCATTCTT CA.... (Gm11) CATGT G/GA....T37020092 B1 S08346-1 136888 37 GGTTGCAATCAAGAG CA.... (Gm11) GGGTAG/GA....T 37020092 B1 S08346-1 136889 38 TGATGATACAACGYC CA.... (Gm11)CCATTC G/GA....T 37311443 B1 S06786-1 144687 39 GCTTTAGACGTGTCC A/C(Gm11) TCCTCA 37311443 B1 S06786-1 144688 40 CCACTTGGAAAGAGT A/C (Gm11)GGGTTA 37311443 B1 S06786-1 S06786-1- 41 AGACGTGTCCTCCTC A/C (Gm11) Q1FAACCA 37311443 B1 S06786-1 S06786-1- 42 AGGAGAACCCTTCAC A/C (Gm11) Q1RACTCG 37311443 B1 S06786-1 S06786-1- 43 CACACTCGCGAGCAT A/C (Gm11) Q2RAGAAC 37311443 B1 S06786-1 S06786-1- 44 TTCAATTTGTTGAAG A/C (Gm11) Q3FCCTTTTCA 37311443 B1 S06786-1 S06786-1- 45 GAGGAGAACCCTTCA A/C (Gm11)Q3R CACTCG 37311443 B1 S06786-1 S06786-1- 46 TAGACGTGTCCTCCT A/C (Gm11)Q4F CAACCAT 37311443 B1 S06786-1 S06786-1- 47 AACCACTTGGAAAGA A/C (Gm11)Q4R AGTGGGTT 37311443 B1 S06786-1 S06786-1- 48 TCAATTTGTTGAAGC A/C(Gm11) Q5F CTTTTCA 37311443 B1 S06786-1 S06786-1- 49 TGAGGCTTTTGAGGA A/C(Gm11) Q5R GAACC 37333894 B1 S06787-1 142755 50 TGCTGTTCCATAATT G/T(Gm11) AGAATTGGAG 37333894 B1 S06787-1 142756 51 CCTGCATCAAGATGA G/T(Gm11) ACAAGAA 37334507 B1 S06803-1 142759 52 GCCAATGGTCCATCA A/G (Gm11)AAATG 37334507 B1 S06803-1 142760 53 AACATCGAAGGCTGA A/G (Gm11) GAACG37334507 B1 S06803-1 S06787-1- 54 GTGTTGTGTGTGCTG A/G (Gm11) Q2F TTCCA37334507 B1 S06803-1 S06787-1- 55 GTTGGCCAATCAATG A/G (Gm11) Q2R AAGGT37334507 B1 S06803-1 S06787-1- 56 GGTTTCAGTTCCACC A/G (Gm11) Q3R ACCTG37334507 B1 S06803-1 S06787-1- 57 AGTGTTGTGTGTGCT A/G (Gm11) Q4F GTTCCA37334507 B1 S06803-1 S06787-1- 58 AGTTCCACCACCTGC A/G (Gm11) Q4R ATCAA37334507 B1 S06803-1 S06803-1- 59 GCTTCAACATCACCA A/G (Gm11) Q1F GCAGA37334507 B1 S06803-1 S06803-1- 60 GAAGGCTGAGAACGG A/G (Gm11) Q1R ACAAG37334507 B1 S06803-1 S06803-1- 61 CATCACCAGCAGAAA A/G (Gm11) Q2F CTGGA37334507 B1 S06803-1 S06803-1- 62 CTGCTTCAACATCAC A/G (Gm11) Q3F CAGCA37334507 B1 S06803-1 S06803-1- 63 TGCATCCTGCTTTTC A/G (Gm11) Q3R TGCTT37117244 B1 S04197-1 142386 64 TGCCTAATGGGAGAG C/A (Gm11) ATGAAG37117244 B1 S04197-1 142387 65 CGCAGGTTCTGTTAC C/A (Gm11) TCGAAG37117244 B1 S04197-1 S04197-1- 66 AATGCCTAATGGGAG C/A (Gm11) F2 AGATGAA37117244 B1 S04197-1 S04197-1- 67 TTTATATTGTAGTGT C/A (Gm11) R2AGGTGCCTTGTC 37117244 B1 S04197-1 S04197-1- 68 TGAATATATAAATGC C/A(Gm11) F3 CTAATGGGAGAGA 37117244 B1 S04197-1 S04197-1- 69TTGGGTTGAAGCCTT C/A (Gm11) R3 TTATGG 37117244 B1 S04197-1 S04197-1- 70ACAAGTAAAGTATGG C/A (Gm11) F4 ATAAGATGTGCAA 37117244 B1 S04197-1S04197-1- 71 TCGCAGGTTCTGTTA C/A (Gm11) R4 CTCGAA 42916770 C1 S07162-1136849 72 AATGCAGGGCCAGTT C/T (Gm04) ACAAT 42916770 C1 S07162-1 13685073 AATTGCCCCCATCTT C/T (Gm04) TTCTC 42916770 C1 S07162-1 80907 74CAGTTACAATACATA C/T (Gm04) CATACGCATAACCAA AACAGTAACA 42916770 C1S07162-1 80908 75 ACTACTGGATTTTAA C/T (Gm04) TGTAGGTTTCTTCCA TGTAGCTATG42916770 C1 S07162-1 87501 76 AACCAAAACAGTAAC C/T (Gm04) ATCAATGGAAC42916770 C1 S07162-1 87504 77 CAAATGGTTGTGTTT C/T (Gm04) TTCTTAGAAATTTC42916770 C1 S07162-1 136845 78 ACCAAAACAGTAACA C/T (Gm04) TCAATGGAA42916770 C1 S07162-1 136846 79 TTTAATGTAGGTTTC C/T (Gm04) TTCCATGTAGC42916770 C1 S07162-1 136847 80 ACGCATAACCAAAAC C/T (Gm04) AGTAACATC42916770 C1 S07162-1 136848 81 ATGTAGGTTTCTTCC C/T (Gm04) ATGTAGCTATG34888681 D2 S07161-1 137370 82 TGCTTATCTTGTCTG A/T (Gm17) AAAACCACT34888681 D2 S07161-1 137374 83 TGACTTTAAGGCAAT A/T (Gm17) TCAACTGTATC34888681 D2 S07161-1 137371 84 ACCTAATGTGATGAG A/T (Gm17) CATCCTTAAT34888681 D2 S07161-1 137372 85 CTTGTCTGAAAACCA A/T (Gm17) CTAATGCTC34888681 D2 S07161-1 137373 86 CTAATGTGATGAGCA A/T (Gm17) TCCTTAATTG

TABLE 3 Non-Limiting Examples of Primer Sequences. Linkage Allele GroupSEQ (Res/ Marker (ch) ID Primer Sequence Sus) S02621-1- D1b (2) 159GCAATTCGTCCTTCC G/A A AAATG 160 GAGTGTGCTTTTGCT CGTTG S01519-1- D1b (2)161 cttgtagcgcagctc C/T A cagat 162 accatgaagtccttg aagcag S08177-1-D1b (2) 163 tttgggaatggagac T/G Q1 agagg 164 gccctattggcattc ttgatS00479-1- D1b (2) 165 TCATGCACTGCCCAT A/G A ACCTAAAGG 166AAACGGATGTGGATG GTTAAGAATTAGAC S02136-1- D1b (2) 167 GGCTGCCGTTTATGT T/CA TGTTAGCAT 168 AGGTATTTAGAATCA GTCCAAGAAGTGAAT TAACT S00875-1- D1b (2)169 ACGCCTCATTATCCG A/G A TGACCCT 170 TTCACAATTCTGTGC AGCCGAC S12875-1-Dib (2) 171 ggacgtggctcaaga T/C Q1 gagtt 172 tgaatgtgatcaaaa gcgagaS12950-1- D1b (2) 173 ggtatgtgcacagat G/T Q1 cctatgg 174 ggcatcatgcaaaacaaaaa S12947-1- D1b (2) 175 ttggtgactgatcac A/T Q1 aagatacg 176tggacaaaaagaagc caaagg S12933-1- D1b (2) 177 tcttaggtcgcaaat G/C Q1cacga 178 tgcaatcatataagg tttcgttg S12853-1- D1b (2) 179 tttttccgcgatcaaA/G Q1 ctatttt 180 acgatccctaattgc tttgc S03246-1- D1b (2) 181tccgacggtattgag A/G A ttaagg 182 gcaacgtatttatgc aactcca S12962-1-D1b (2) 183 ttgccatggaagggt A/G Q1 aaagt 184 tgcaccactgcaatt agtttgS00144-1- D1b (2) 185 AGCTTCAGAGGCACG G/C A ACTACCAG 186 GGCACCATCATCTCCACCAATC S08166-1- D1b (2) 187 ttgaattccacacga T/C Q1 catttg 188gagcgttatggggag ctaga S01081-1- D1b (2) 189 aacagctttagcctt A/C A caacca190 gttgtgtccaagaag cagca S02183-1- E (15) 191 caggctcgYagtagt A/G Atagga 192 ccaacctctGtagca a S00350-1- E (15) 193 TTCCTTTTAATTTGC G/C ACCAATGTGAGA 194 TCCTATGTTAGTCCC AGCATGAAACTTC S02074-1- L (19) 195ccttccttgatatct A/G A tgaggttg 196 cattacaatgtgtgc cctgtg S03991-1-L (19) 197 ctgtcagccatgtcg A/T A atttc 198 ctgccagcaaaaaca gctaaS04785-1- B2 (14) 199 tccgaaataaggcac T/C A ctgtt 200 ttgcgtgagtttgggtatga S02874-1- B2 (14) 201 gcatggtcttgcacc T/G A ttttt 202catggctcatttccc ttgtt S04348-1- B1 (11) 203 caatcacaccaccac T/C A caaga204 ctttgacaaggccat cgagt S01209-1- B1 (11) 205 ttcctgaagagcgga A/G Agacag 206 gcacggagcttctca taagg S01999-1- B1 (11) 207 ccccaaagtcggagaT/G A agaat 208 tgttatatgggaggg ggtga S04937-2- B1 (11) 209gcttcttgactttat Null/C A crttctctcc 210 agctagggaaggatt tgggta S04937-1-B1 (11) 211 TCAACCGTGGAAAGT A/G Q1 AACCA 212 TCAATTTAGTTCTTGAAAGTTGGAGAC S04938-1- B1 (11) 213 ccacaacctattgtt G/A A gaagcac 214tgtgcactcctgact gcttt S04938-2- B1 (11) 215 tcaaaaccattgttc T/G A atctgg216 gaatagaagatgaca acrcattaaagat S06786-2- B1 (11) 217 cggacaaggtcctgtG/A Q1 aaggt 218 ttttgtggattgaat tcatggt S06786-3- B1 (11) 219tgcaaacactgtaaa C/T Q1 taacactaatagg 220 aaatggttgaggagg acacg S06786-1-B1 (11) 221 agacgtgtcctcctc A/C Q1 aacca 222 aggagaacccttcac actcgS06787-2- B1 (11) 223 attgctggatgtgag A/G Q1 gttcc 224 tggccaacaaggatgaaaat S06787-1- B1 (11) 225 tgctgttccataatt G/T Q1 agaattggag 226cctgcatcaagatga acaagaa S06803-1- B1 (11) 227 gcttcaacatcacca A/G Q1gcaga 228 gaaggctgagaacgg acaag S06804-1- B1 (11) 229 aggtactgtcctagcC/A Q1 ttcag 230 gccaataaagcttgg tggaa S06788-1- B1 (11) 231aagaaaccccaccaa G/A Q1 taggg 232 aacggatcagggaac attg S06805-1- B1 (11)233 gatgaaatgtactgg T/C Q1 cttgaaatta 234 cctggaaacttgcat gagtgS06789-1- B1 (11) 235 cgtcagctattccac A/G Q1 ccttc 236 ggtgagatcaagagggcatt S06790-1- B1 (11) 237 tcctgaaatcccaag T/G Q1 caatc 238cttcaatgggtcgca aaaag S06791-2- B1 (11) 239 atgcggaagatcaay A/T Q1 agcag240 atgcagacccaattc atgct S06791-1- B1 (11) 241 acaacgwaaggtatg C/T Q1aggtcaa 242 atcggtgagcaaggg aaac S06792-1- B1 (11) 243 tcaaccaaaagatccC/G Q1 cacc 244 gcagccacctaacag aacaaa S02112-1- C2 (6) 245CATGTTGCTCGCGAC A/G A CTTGAC 246 GAAGGTGATTGAGGT GGTGAAGGA S03252-1-C2 (6) 247 gcttggaatattaat G/A A ctatggctgt 248 cgcgttacaaattaa agcatgt

TABLE 4 Non-Limiting Examples of Probe Sequences. Linkage Marker GroupProbe 1 Probe 1 Probe 2 Probe 2 Position (ch) Locus Name Sequence NameSequence 37220579 B1 S04196-1 141540 ATTCCTAAAGATAGTCCAAT 141539CTAAAGATACATGCAAGTC (Gm11) (SEQ ID NO: 87) (SEQ ID NO: 88) 36954994 B1S04938-1 S04938- TTCTGATAGACGAAACC S04938- CTGATAGATGAAACCCA (Gm11) 1-P1(SEQ ID NO: 89) 1-P2 (SEQ ID NO: 90) 36954799 B1 S04937-1 141537CAAACTGCAAGATT 141538 CACAAACCGCAAGAT (Gm11) (SEQ ID NO: 91)(SEQ ID NO: 92) 36781754 B1 S08344-1 102404 CGGAGAATAAATAAATAAG 102405CGGAGAATAAATAAGTAAG (Gm11) (SEQ ID NO: 93) (SEQ ID NO: 94) 37020399 B1S08343-1 102406 TTAGTGGACAGTGCCA 102407 TTAGTTGACAGTGCCATA (Gm11)(SEQ ID NO: 95) (SEQ ID NO: 96) 37020092 B1 S08346-1 102384TTTGTGAAGAAAAATATGAAA 102385 TTGTGAACAAAAAGATGAA (Gm11) (SEQ ID NO: 97)(SEQ ID NO: 98) 37311443 B1 S06786-1 142753 CTCAGTATATCATCTTC 142754CCCTCAGTAGATCAT (Gm11) (SEQ ID NO: 99) (SEQ ID NO: 100) 37333894 B1S06787-1 142757 CACCTAAGGAACAAT 142758 CCTAATGAACAATACC (Gm11)(SEQ ID NO: 101) (SEQ ID NO: 102) 37334507 B1 S06803-1 142761CTTCCAGTGGCTGCT 142762 CCTTCCAGCGGCT (Gm11) (SEQ ID NO: 103)(SEQ ID NO: 104) 37117244 B1 S04197-1 142389 CTACTACCATACCTAAAC 142388TACTACCATCCCTAAAC (Gm11) (SEQ ID NO: 105) (SEQ ID NO: 106) 42916770 C1S07162-1 102396 AATAGGACACAATTATTA 102397 ATAGGACACAATCATTA (Gm04)(SEQ ID NO: 107) (SEQ ID NO: 108) 34888681 D2 S07161-1 125316TCAGTGAGAATAAAA 125331 TCAGTGTGAATAAAA (Gm17) (SEQ ID NO: 109)(SEQ ID NO: 110)

TABLE 5 Non-Limiting Examples of Probe Sequences. Linkage Group Probe 1SEQ Probe 2 SEQ Marker (ch) Sequence ID Sequence ID S02621-1- D1b (2)CTCTATTA 249 TCTATTAC 294 A CTaTCTGT TgTCTGTC CTTT TTT S01519-1- D1b (2)acaggaCg 250 acaggaTg 295 A atactc atactcac S08177-1- D1b (2) ctttgcat251 ctttgcat 296 Q1 ttTagatc ttGagatc at a S00479-1- D1b (2) CAAGTGAT252 CAAGTGAT 297 A GTTtATTT GTTcATTT T T S02136-1- D1b (2) actcgaaT 253ctcgaaCg 298 A gtactctc tactctc S00875-1- D1b (2) TCAAGATC 254 TCAAGATC299 A ATtCACTA ATcCACTA TT TT S12875-1- D1b (2) ccacgtAt 255 ccacgtGt300 Q1 tgttctt tgttct S12950-1- D1b (2) ccagcctt 256 ccagcctt 301 Q1Cgtagca Agtagcag S12947-1- D1b (2) aaaTtttg 257 aaaAtttg 302 Q1 tgctatcctgctatcc ac ac S12933-1- D1b (2) tcaaacaC 258 tcaaacaG 303 Q1 tgattctctgattctc S12853-1- D1b (2) atgctacc 259 ctacccgt 304 Q1 cgtgtAtagtGtatac t S03246-1- D1b (2) cctatgct 260 cctatgct 305 A atcAgtttatcGgttt t t S12962-1- D1b (2) ttgaaTgg 261 tttgaaCg 306 Q1 tctccacagtctccac tg S00144-1- D1b (2) TTCACAAG 262 TTCACAAG 307 A TgTATAACTcTATAAC C CT S08166-1- D1b (2) acatctcc 263 catctccc 308 Q1 cacTggcacCggc S01081-1- D1b (2) caaccatg 264 caaccatg 309 A Actttc CctttcS02183-1- E (15) ccaacctc 265 ccaacctc 310 A tAtagcaa tGtagcaa S00350-1-E (15) TCTTTcAC 266 TCTTTgAC 311 A AATCTAC AATCTAC S02074-1- 1 (19)ctactctt 267 ctcttgcg 312 A gcgTtgtt Ctgttaa S03991-1- 1 (19) tcaaacAa268 tcaaacTa 313 A ggatctcc ggatctcc S04785-1- B2 (14) attctggt 269attctggt 314 A Tcttcact Ccttcact tg t S02874-1- B2 (14) cctcacAa 270cctcacCa 315 A attacca attac S04348-1- B1 (11) acaaaTgt 271 acaaaCgt 316A acaccgcc acaccgcc S01209-1- B1 (11) cttccaga 272 ttccagag 317 AgcagTgc cagCgc S01999-1- B1 (11) catacccc 273 ccataccc 318 A TtacaagccGtacaa S02112-1- C2 (6) tcctatgT 274 tcctatgC 319 A tggtctgg tggtctggtc t S03252-1- C2 (6) ttggcttt 275 ttggcttt 320 A gaatCac gaatTacS04937-2- B1 (11) ccgaacgt 276 ccgaacgC 321 A gtcatat tgtcat S04937-1-B1 (11) caaacTgc 277 cacaaacC 322 Q1 aagatt gcaagat S04938-1- B1 (11)ttctgata 278 ctgataga 323 A gaCgaaac Tgaaaccc c a S04938-2- B1 (11)attaactT 279 attaactG 324 A ccttcttt ccttcttt tac S06786-2- B1 (11)ttacttgG 280 acttgTTa 325 Q1 Caacaat acaatgtc ac S06786-3- B1 (11)caatttGt 281 caatttAt 326 Q1 tgaagcct tgaagcct tt S06786-1- B1 (11)ctcagtaT 282 ccctcagt 327 Q1 atcatctt aGatcat c S06787-2- B1 (11)aagccacg 283 aagccacg 328 Q1 agTcat agCcat S06787-1- B1 (11) cacctaaG284 cctaaTga 329 Q1 gaacaat acaatacc S06803-1- B1 (11) cttccagT 285ccttccag 330 Q1 ggctgct Cggct S06804-1- B1 (11) ctcacCgg 286 caacttgc331 Q1 agcaat tcacAgga S06788-1- B1 (11) ctaacctc 287 ctctctaa 332 Q1Cagaacac cctcTaga ac S06805-1- B1 (11) cacttgTc 288 acacttgC 333 Q1tttacaac ctttacaa at c S06789-1- B1 (11) tctctatt 289 tctctatt 334 Q1Ttccgaaa Ctccgaaa tg tg S06790-1- B1 (11) ccacattt 290 ccacattt 335 Q1Tcttcc Gcttcc S06791-2- B1 (11) accttAcg 291 accttTcg 336 Q1 ttgtagatttgtagat c c S06791-1- B1 (11) ctgctGtt 292 ctgctAtt 337 Q1 gatcttgatcttc S06792-1- B1 (11) acgaacaC 293 caacgaac 338 Q1 gtcctga aGgtcct

TABLE 6 Non-Limiting Examples of Genomic LociComprising the Various Marker Loci Provided Herein. SEQ ID Marker NOPosition Locus (Res/Sus) Reference Sequence [Res/Sus] 37220579 S04196-1135/136 TGCCATCCTAGCTAGCCCTGTATATTTTGATTANNTTNATGGGAAGAAAAAATTAAATATTTTTATTTAATTGAAGAGTAAGTTAATTTTATGAAAACAAAAATTTAACATTTTCTTACTTATCTTTTAATTCAAATTTTATTTTATTTTCTCTTATTCCAACAATAATTCCTAAAGATA[*******/CATGCAA]GTCCAATATGTTTAACTCATCACATTTAATTTCATTACGAAATAATCAACAGGTCAAGATAATTTTAAGACAAATTAGATTATAAGGATTGTTATTTTCTTTTAAAATATATTATTACACAACTTTTGTCATATATATTATGCGCCCGATGCCTCGATGACACCTAACACATATATAAAACCTTTTTTATAATTAAGAATTAAAAAAGAGAGAGAGAGGGAAGAT 36954994 S04938-1137/138 AACAGCTATGACCATGCGAACCTTCCAAGGACCAAAATGAATTTTCACTCTAAAATTTATGTGCACTCCTGACTGCTTTTACATTTAGTGTCTTCATTTCATTGGGTTTC[C/T]TCTATCAGAATTCAGTGATAAGAAACAGTGCTTCAACAATAGGTTGTGGAACATGTTTTTCTGAGAGGTAAGGTAGTCACAATGAAAAAAAGGACAAAACTTAGATCCAAAGCTATGTTGCATTGATTAACAAAGTAATCACATAATTTTGGTGTCATTTTCTAATAAGAATTGGAGTTTCATCTTGAAAGTTTATGTTGACCTGTAATGCAAACCTGTATTGCATAGATTAGTGAAGTAAAACTTTGTTTTTTATTAGAGAATAACATCAAAAGCATTTATGGATCTGCATGAGTTTTTCCTAAAAAGGTGTGAAATAGGGGGAAAAAAGCCACACTGGATGTCAAAACCATTGTTCATCTGGTATATATTTTCATCTCCWTATGATARTTTTTTTTTCTTTTCTGATTTCTTGTGAAATATATTAATTAACTKCCTTCTTTTACATGTAAATGAGAATGTTGTTAATTAATATGTTAACCTAAACGATATCTTTAATGYGTTGTCATCTTCTATTCGTT TTGCAGTGATGGTATCC36954799 S04937-1 139/140GAATGCTTGTTTCACGTAAGCTTCTTGACTTTATCRTTCTCTCCCCCGCCCCCCAAATACCACAAAAATTCCGAACGCTGTCATATTGCAATCTAATTGTTTAATACCCAAATCCTTCCCTAGCTCTTTTCCAGTATCTTGAGCTTGTAATCTTCCATCTTAAAAGCATACTGACTGATGCAATCTTCTGATTAATTTAGACCTGCATCAGTTACTTGCTTGCAAGTTGTAGAATCTCTTATTTTYCTTTTCACTTCACTGGTTTGCATGTCCATACAATTCGAACTATTTTTTATCTTTCAAAGATTGGAATGACATTAACTTGGTTTTTGATCCTAATAGATAAGTCATATCAATTTAGTTCTTGAAAGTTGGAGACTRAATGTCCTCTAAATAAATTGACATCAATGTAGATCCTCAATAATAGAAAGATGACATCAATTTASTCCCTAAATCTTGC[T/C]GTTTGTGCATAGAAGGATGGTTTTTTGGTTACTTTCCACGGTTGAGGTACTAAATTGATGCAATATCTCTTAGGGAGTTAGAGGACAAAGTGATGTCTACCGAACCTTCCAAGGAACT GGCCGTCGTTT36781754 S08344-1 141/142AATCCCTCGTTCTTCATGCCCCCCAACCCAACATTCCCAGTCGACACGTCTTCTACTCCTTAATTTCCTCCTTCTTTCAAACTTGACAAAGCCACAACTCTTCTCTCATCTCATATAAATACCCTTCCACGACACCAATTTCTCCATCCTCTCATTGAAAAACAAAATTAATCATCTTA[C/T]TTATTTATTCTCCGAAAATGGTTGATTTACATTGGAAATCAAAGATGCCAAGTTCCGACATGCCTTCCAAAACTCTAAAACTCTCTCTCTCCGACAACAAGTCCTTACCCTCTTTGCAAC 37020399 S08343-1 143/144CAAGCAAACTTAGACTTACCAAATGAGTTTGACCAGGTTTTACCCCTCTTGATTGCAACCTCACGACCATCAACGAGTTTGCCTCTGTACTCAACAACAAAGCCTCCGGTACCAATCTTGTTGTCAAATGAGAAATTATTGGTGGCTGCTTTAAGTTCAGCGAGGGTGAATAATGGTGCAGCAAAAGCATGCACTGGGGAAGGGGATGATYCCAAATCTGCTTCACTGGCACTACTACTCCTTATGGCACTGTC[C/A]ACTAATGAAGCAAAACTACGGACACGAGATTCTCCAAAAATGGACCCAGTATCACTCCTTATGTCGCTGTCGACTGCCATGCTAAAACTCCTTGCATCATCTGTGTTATCCCTCACATCAATTCTCTCAACGGTTTCAGTATCCATTTTATTTGATTTGGTAAGTGAAAGTATGTACTAAGTGCTTTGGCAGAGGCACTGAGCACATATRTCATATACAGAGACCAAAGCACATACATATATATATATATATTAATTGAG 37020092 S08346-1 145/146CTTCNCNGCACCTTCTCAATTAATATATATATGTATGTGGTTTGGTGTCTGTATATGACATATGTGCTCAGTGCCTCCGCCAAAGCAAATAAAATGGATACTGAAATGGTTGAGAGCATTGATGTCACAGATGATGCAAGGAGTTTTAGCTGGGCAGTGGACAGCGCCATAAGGAGTGATACTGGGTCCATTTTTGGAGAATCTCGTGTCCGTAGCTTTGCTTCGTTAGTGGACAGTGCCATAAGGAGTAGTAGTGCTACTGAAGCAGATTTGGAATCATCCCTTGTCCAGGCAGAAGACAGGGCGATGAGGACTGTTGCAGCACGATTAACAAAAGCCGTGTCAAATGCAAAAAGACATTTTGCTAAAGGATTATTTACCCGGGCTGAGCTTATACCAGTCACCCAGGCTGAGCTTGAACCAGCCACCAACAATTTCCMRSSAYYAWTAWTTWCYCWKKATSACCWYARMKCCAGCCACCAATAATTTCTCATTTGACAACAAGATTGGTACTGGAGGCTTTGGTGTTGTTGAGT:ACAGAGGCAAACTCATTGATGGTCGTGAGGTTGCAATCAAGAGGGGTAAAACCTGGTCAAACTCATTTGGTAAGTCTRAGTTTGCCTTGTTCTCCCGYTTACACCACAAGAATTTGGTTGGGCTGGTTGGATTTTGTGAA[C/G][A/A]AAAA[G/T]ATGAAAGGCTCTTGGTGTATGAGTACATGAAGAATGGGRCGTTGTATCATCATTTGCATRRCAAGAAGGGTARCAGTGTGTTGAATTGGTAAAWANRYG RASRWRGSWATSWGTGK37311443 S06786-1 147/148STATTGCACSCGCTTTTCGTCCCGGTCAAGAAAAGATGGTTTATGTGTATCAGCTCTTGGCAACAGGCACATTGGAGGAAGATAAGTACATAAGAACCACTTGGAAAGAGTGGGTTACTAGCATGATTTTTAGTGAGGCTTTTGAGGAGAACCCTTCACACTCGCGAGCATAGAACATTGAAGATGAT[A/C]TACTGAGGGAAATGGTTGAGGAGGACACGTCTAAAGCAATTCATATGATTCTAAAGAATGAAAAGGCTTCAAYAAATTGAAGAGAGGTAATTACGCTTTTTTCATATGAAAACATGTGCTTAATTTATGTTTATATATCTTAATCCTACATTCTCCCTATTAGTGTTATTTACAGTGTTTGCACTAGATCACTAGAATGCTTGTTGGCATTCACCTTCAGTGTTGGAGACAGATTTGACACTTGTCGTCTCGAATGCCAGGGCAAGTTCGAGTTTAGTAGAAACTTATCATCCAAAATTAAAATTGAAAGCACTAATACAAAATGCACAATTTGAAGCCATTCATGTCCTCTCTTGGTCTGAGTCTTGTCATTTTGTGGATTGAATTCATGGTTTCTCTTATCCGGTGACATTGTTRMCAAGTAATACTACTATAAATTCAGATTTGGATATCAGATAACCATGGTCATTAATAGTAATACTAACATACTATACATATAATACCTTACAGGACCTTGTCCGAAACTTGAAACAGGATCAGGGACAGCGAAAAACAAACATGGTCAWAnCYKKTTYY 37333894 S06787-1 149/150TTACAAATAGGAGAAAACTTAGATATACATAGTTCTTTAAGTTTGATTACATTACAAATAGGAGAAAACTTAAACATACATAGTTCTTTAAGTGTTGTGTGTGCTGTTCCATAATTAGAATTGGAGTTTTACTTACCTTAGTAATATGTATAATTCTAATTGGAGAACAGTACAAACAAAAACACCTAA[G/T]GAACAATACCTTAGTTTTAATCATATTTGTTTTGTTCATATAGCTTATCAATAAGTGAAGTATTTTCTTGTTCATCTTGATGCAGGTGGTGGAACTGAAACCTTCATTGATTGGCCAACAAGGATGAAAATAGCACAGGACATGACTCGTGGCTTGTTTTGTCTTCATTCCCTGGAGAACATTATACATGGGAACCTCACATCCAGCAATGTGTTGCTTGATGAGAACACAAATGCTAAAATTGCAGATTTTGGTCTTTCTCGGTTGATGTCAACTGCTGCTAACTCCAACGTGATAGCTACTGCTGGAGCATTGGGATACCGGGCACCAGAGCTCTCAAAGCTCAAGAAAGCAAACACTAAAACTGATATATACAGTCTTGGTGTTATCTTGTTAGAACTCCTAACTAGGAAGTCACCTGGGGTGTCTATCATGGTCATAG CTGTT 37334507S06803-1 151/152 TTGCGTAATCTTTCTGTTCTGATTTTGAGTAGGAACCAATTTAGTGGACATATTCCTTCAAGCATTGCAAACATTTCCATGCTTAGGCAGCTTGATTTGTCACTGAATAATCTCAGTGGAGAAATTCCAGTCTCCTTTGAAAGTCAACGTAGTCTTGATTTCTTCAATGTTTCTTACAATAGCCTTTCAGGTTCTGTTCCACCTCTACTTGCCAAGAAATTTAACTCAAGCTCATTTGTGGGAAATATTCAACTATGTGGGTATAGCCCTTCAACCCCATGTCTTTCACAAGCTCCATCACAAGGAGTCATTGCCCCAACTCCAGAAGTACTGTCAGAACAGCACCATCGTAGGAACCTCAGTACCAAAGACATAATTCTCATAGTAGCAGGAGTTCTCCTAGTAGTCCTGATTATACTTTGTTGCATCCTGCTTTTCTGCTTGATCAGAAAGAGATCAACATCGAAGGCTGAGAACGGACAAGCCACGGGGAGAGCAGCC[A/G]CTGGAAGGACAGAAAAAGGAGTCCCTCCAGTTTCTGCTGGTGATGTTGAAGCAGGTGGGGAGGCTGGAGGGAAACTAGTCCATTTTGATGGACCATTGGCTTTTACAGCCGATGATCTCTTGTGTGCAACTGCTGAGATCATGGGAAAGAGCCATGGTCATAGCCTGT 37117244 S04197-1 153/154TTTCTTAAGTTATATGTTATTTCATTTAAGTCCTAACTGTCNNTTNACTCCTCTTCTTGCTATTGTCATTAGTATTCACTTNNTTTNAATAACTGTGGAAGCAAAATGATCGTTGTGTAATTTTTTATTGTATATTAGATTATTAGGTTTATAATGTTGTTTTGTTATGTTATATATTTGAATGACTCGAGTTTATGTTTTTATTTTTAATGCTACGTTTGGATGATTTAAGAGTAAAATATTAATTTATTTATAGTAAATTTTTTAATTAATATTTTGTATTCATTGGTTGAATTTATAACAAGTAAAGTATGGATAAGATGTGCAATAATGAATATATAAATGCCTAATGGGAGAGATGAAGATTAAAGTTATTATTATATACATAAATATAAAATTGGAAATGAATATTTGTTTTAAATGGAGTATGAAGATCATACCCTATCCAGTATCTACTACCRGTATCTACTACCAT[C/A]CCTAAACTCGACAAGGCACCTACACTACAATATAAATATAGTAAGGCTTCGAGTAACAGAACCTGCGACATATAATAAGCCATAAAAGGCTTCAACCCAAAGACCCTACGTTACGAGAAAAGAAGAAAACATTTGTTGAAGTGAACCACAACAACGCAATGGCATGGTCAT (CONSENSUS) 42916770 S07162-1 155/156CGCAATTAACCCTCACTAAAGGGAACAAAAGCTTGCATGCCTGCAGCAATATAACCAGGATTCAGAATTAATCTAGTTAGTATATCATACAATGCAGGGCCAGTTACAATACATACATACGCATAACCAAAACAGTAACATCAATGGAACAGTAATAGGACACAAT[C/T]ATTATTATTTTTTTGTTAAGGAAATTTCTAAGAAAAACACAACCATTTGTACAAAAAAGGTATTAATACATAGCTACATGGAAGAAACCTACATTAAAATCCAGTAGTGAGAAAAGATGGGGGCAATTATGATAATCTCGGAAAGCCTCTGCCAAGGGTCAGCATTCAAAATTGAGTTCCTTAGCCTGCTGTCTGCATATGCTTATCCACAAGGAATATTGTCTCCGTGAGGATTAACCAAAAGCATACCTCAATGGGTCCAGATATCCTGAAGATAGCGCCCAATTTGCTGAGCACCAAAATATAGGGCATCGGCAACGAGAAAGACTCCAATCTACGCCACAAATGTCAAACTTGTGAATGTCAAGGTTAAGAAATAAGATTTACAATTGAAGGTCTACAGCAGATAGATTACCAGGCGTGCAGAAAACACTAATCTATATCCCCAACCTTCCTTGGCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCGCCCTATAGTGAGTCGTATTACACCCTATAGTGAGTCGTATTACGCCCTATAGTGAGTCGTATTAC 34888681 S07161-1157/158 CTTG:AAGTTATAAGTTTTGAGAGAGATTTTATGCTTATCTTGTCTGAAAACCACTAATGCTCTCTTCAGTG[A/T]GAATAAAAGGGCTACAAGATATCATACATATGCTTTAATATTATATCACTAAATACAATTAAGGATGCTCATCACATTAGGTTAGGTTAGATACAGTTGAATTGCCTTAAAGTCAAAATTTCCACAAG:::AC:::AACAGTAACAGTTACCAAAAACCATGCCCACAACAAGCAATATTGGCTGCGTGACTTAAAAACTGTTTAAACATCTCAACTGATGTCTTACAAGGAAAGGTAACCTAATGAAAAGACATCAATCTAGAAATCAAGGCACTTCAGTGAGAAGACAAATGAAGTCCAACTGATTGCATTTTGTCTTGTCATATTAGGACTTAACATTAGAAGCAAGTTGCATATAGAACAAATCTGAAGGATCATTTTATATATATTTAACAACTACTGGTTGACCACCCAATACGATAAACAGGAACAACCACACAAAAGCTCTTGATCAACATAAAGAAAACAAAATTAAACACAAAAAACTGCTACAGAATTTAAAAAACACTTTAGCAGACGTAACAGAAGTACAGAACAAATTCTGTCAGCAATTAAGCTAACTAGATACCAAACAGGATACTTCCATTGTAGTAGAAAAGGTGAAACACTATAGAAAAATTCAACAGTCTAGGTGATTAAATCTAGACTCAAATCTCTCAATGTATAAATGGTCCTCTTAAAAACCAACCCTGCCAATGGTAGCAAATCCCCTGGACATAATGAAGCACACGAACCAACAAAGAATCCAATAGAATAAAACCAAAAACCAAAAAACTTAAAGTCCAAACAACAAATACACAGGCAATCAAATCAACCAAACAAAATGATGTACACACATACACAAAATGATGTACACATACATATAATTAGGCTTAAATATGTTTTTGATTCCTTAAATTTGGAGTTTGAACAATTTTG

TABLE 7 Non-Limiting Examples of Genomic RegionsComprising the Various Marker Loci Provided Herein. Locus SEQ Name ID NOSequence S02621 339MMRGCTATGACCATGGGGAAGTGCATGAGTGCTTTTTCAGATACCTACTTATAAGTAGGTTTGAATTAAATTGATTATATTGTCCTAGTAGAAGTGGCTATATAATATTTTTTGAGTGAGTGTGCTTTTGCTCGTTGCATGATATAGCAGATATGCTATCTGAATGCTAAAGGTACTCTATTACTRTCTGTCTTTTCTTCTCATTCCTTATCCATACATATTTTGAACCAATTTTACATTTGGAAGGACGAATTGCTGCCAATGGTGCAATCTAGCAATCTTACCTTGTCATTTTCAACTGAAAGTTCAATTGAGGAAGAACTAAAGAGAGAAAGCACTGCAGATGTCATAACAATACTCGTAAGAAATTTCTGTTTCTTTCAACTAAATGTGAAAACATGATTTGTGTTGTGTGTAAGCTAATGAACTGATTAGTTTGGTTGTGGCTTCATAAAGATGTGCTTTATTGGAATATACAATAAATGTCTTCTCCAACATATTATTAGGTGAGCTATATTGTAATGTTGCTT A S01519 340GatGGGTAGACCAATACACAAGTTTGCAAGCATTGTAGGATATAGAGAGGGTAAGATGTATACAACTTTACCACCATAAGAAGAGAGGCTGCTTCTGAGACTAGAAAATTTGACCACCAGGTCACAAGCTTACAACCTTATAACTGCACGAAGGTTTACTTTCTAATATGAAGAAATACCACCTTTTGTCATGTAAATATTTAAGTTTACTAAATTGAAATGTTGATAACAATGCAAAGAAAAGAGTAGTCAGTGACTCAATTCAAAAGTTGATGATACCAAACAAACCTGAAGCTTGTAGCGCAGCTCCAGATTTCATGATTGGCTCCCCAACAGGAYGATACTCACAGCCTGCTTCAAGGACTTCATGG T S08177 341AGTACCAAGGGAGGACATGCATTGTGTTGCACAGTTTTTTTCCAGGACATGGGAACTGCAAGTGCTGGTTGCTGCTTGTTTAGCCCTTCCATGATAAAAGAAAATGCCCCAAAAGTGAGACAGCTCTGCAGAAGAGCTTGTGGTGCACCTGTAAAACCCTAGAATATAAGTCCTAATAACAAAACAAGTACACAGAATGAAATTTACATGTGTATTTAGCTGAACAATGAATTGTTGAATTTTAACAATAGCAATGATTGGAAGCCATTCTGAGTCAGCAAAATTTCCCCCCTCCTCCATTTAAGGTGATGGTTTGGGAATGGAGACAGAGGATTCCAGAGTAATACATCTCAAGAAACAAATTACCACACTGATTATGGACAAAATTATCTTTGCATTTKAGATCATATGACTATGCTTTTAAAGAGAGATCAAGAATGCCAATAGGGCCTATTCAGAATAGTCAGATTGGCAAGTCCTTTATCCTAATTCTTTCTTATAGATTTCAAAAAGAGGGCAAACCCATCAATTTGAATAAATAAATAAGAGATACCTGGAAAACTTAGAGCAAGACCAGTGCAACATCCAGCAACACCCGCATTAATGACTGCAAATGCAAAAGAATTCACATTACCAGAGGAAGATCACTTAAAAGCAAAAGTGACAAATTTTACAACTAAATATTCATACCATCATCTTTTCCTCTAAGCCTTTTCAAGATGCAAACAACCAAACTATGAACTCCAGACAAAACTGCAAATGTCTAATGACATAAAGAACAACACAATTACTTAC AATCTA S00479 342MTgcaTGCATGGATTTTAAGCAAATAAATTAATGTGAAGTATTTCAATGTATGCCCGTGCMYHKAHCACATCTCATGCACTGCCCATACCTAAAGGATAAAATATCAAGTGATGTTYATTTTTTAATCTCCCCTTCAAAATGACCAATTAATGTAGAGAACCTTCTAAGTTCTATAGATTTTAACACTTGTCTAATTCTTAACCATCCACATCCGTTTCTCATGTACCTTTATAGTTTCAATTATTTCAACAATAACGCCAACACTGTAAAGTTTTTGCCGTTACCAGTTCCAAATTCTACCTTTTTTCTTTTCTGTAACAGCTGGATTCACTGTACTAAAATCCAAAAAGTGTCTGAAACCGGAGTTTGTCTATTTGCCATGGTcaaRBBBDDTYYCYVVBDDBBRBRDVBBVDBDBVBBHDVMVBBBRVHDDVVDDRDRBBRVVDDBBBWBVHBWBBDHHHWBYBMBHDHBBBMBBHRBHBWBBBBBVBBBBDRBBDRBBKRBBDVBBDWDWKKWDWSaMaRKD S02136 343ATTTTATTTTATTTTTTCTGAGATAAACAATGAGCCAATAGTTTAAAATGGCTGCCGTTTATGTTGTTAGCATATAAAGATTCTCAATAATATTCAATTACTCGAAYGTACTCTCTAAAATAAACAAGTTAATTCACTTCTTGGACTGATTCTAAATACCTGTTAACTGCAGCATATAACCTGTACTAACTTCCCAATTTAAGAGTAATCTAACAAACAATATTAAGAATTTTATAATGCAAATAGACAGAAAGAATCTTACTCCCACATGGTTAACTATTTTAGCCTAGGTGGTGCATTGTAATTTGCTATTATACAGTAATTTTGTAATTACARTACATAGAAAAAGGTCAAGAGTAAGTGAATTAGATTTTAGAATTAATAGGTGCTGACACTATAGATCCACACCTATGAAGGTCTCCAGGTTGTCCTGATGAGGTCCTAAACTTACCCATATGCCATGCATGTCTGACAGAATGACACTTCACCACCACATGGTCATAGCYKKKT S00875 344tCgCGaccATCcaAGAGTTTGCCTTTATAAACAACACCATAGCTTCCAGCACCAATCTYTCAatCAAGGGCGAAATTATTGGTGGCAGCAACAAGCTCAGCCAAAGTGAACTCCTCAGCCCTCTCAGGATGCTTTGTGGATGATGTTCCACTCCTTTGACGCCTCATTATCCGTGACCCTTGACGCCTAATAGTGRATGATCTTGAAGGAGGACTAATGCTATTATTAGAACCACCCACACCATTTACACTGCCACCTCTAGTGATTGTCGGCTGCACAGAATTGTGAACTTTCTTCTTCCCAAAACAAACCCCAGTCCACAAACAATAAATCGCAGTGCATATCCCAGCAACACCTCCCACGCATCCAACAATGGCAAATGCCAACAACCCCTTAGTCAAGGCCTTCGACCGAGAAGCTGCAGGCCCCGGTGGTGATGCTGGCACCACCGCAGGTGGAGCCGGCACCAGCATTTCAGGCCAACAAGCATGGTcaTAgaatGTTTccaa S12875 345TAAACAGTTTTCTAACTAGTGAAATTTCATTTCGGTATCATTGGAAACGGAGAATTCCAATATAGCAGAAAACATGAACAGAACGCGTTGTTCCAAAGCAAAGCCAATAATAACTCACAGTGTTCCCACTGCTAATAGACGTTGAATGTGATCAAAAGCGAGAATAGACGCATTAGATGGAACGCCATAGTGAAGAACAAYACGTGGATCAAAATTCCCCGACGGAAAACTCTCTTGAGCCACGTCCTGTTGCTGAACGGCGCGAAAAATGTTCAGAAACAACGTCAGCTTCAGGATTTGCGTTCATATATAAATAAACTTCTACGAATGCACTATTATTATCATTAAAAAAAAACAAAAAACAAAAGGCTCCCTAGCATTATTCGTAACCGCAAGAAAAA S12950 346TCGGCGCCCAATTTCACCCTGAAAAAAATACATATAGATGTAGGGGAAGACCTAAAAGAAGAAATTAAATCAAACAGAAACATAGGAGACAAACAATTTAGTAAATTGAGAAACATAGGAGACATAGGTATTATTATTTAGAATGAAACGGCATCATGCAAAACAAAAAAGAATCATGAAAGAAATTTATGCACTGCTACKAAGGCTGGTTTGTTCAAAATACAGACCATAGGATCTGTGCACATACCAGACAGATAATATCATGCAAGCAAACAACTTTGATAAACCAATTCCTAAACACACAAGTGCACAAATGATAATAGATTATAAATATATCAAAACTTCAAGCTAATTGCATATAATGGAAGTGGAAAGAGGAAACAATAATGTAAAACATAGTA S12947 347AACTGCAAAACATAATGGACCAAGACATTAAGCCATTTTTAAAATAGTCCAAGTTCTGGACAAAAAGAAGCCAAAGGGTTAATTTAAAAAAAAAAAAAAAAATTGTAATCTTTTTTCCTAGATCCTTTTTTATAAATGTTACACAACATAAAAGGTATAGTAGTAAATTTTGCAGTGTATCAATTGGTGGATAGCACAAAWTTTTTTTCGTATCTTGTGATCAGTCACCAAACAGCTCCTATACAAATAATATCCTGTGACTCAACGAGTTGAAATGTGCTGTTTTGTTTGTTTGTCTCTCCATACACATCAAATACAAAAAATTATACAATTTTACATAAGTGGAGGGCAGGGAGCACAACCCTCACTCTATGAGCTGGCTATTGGAGTTGAGTTAGGCT S12933 348AAGACCTAAAAAATTATAATTTTTTTTTTTATAAATTTTAGTCAATTATAAAAATGATACTCAAAAGAATGTGTTAAAAAGTATGTTATCAACATTTTTTTAATATTATATACATATTTCTAACACAAATGATTGATGCAATCATATAAGGTTTCGTTGTGTTTATATAAGTGAAAACGATCTAGTTAATATGAGAATCASTGTTTGATTCCCACTATTGCAAAATTTTATCAAACAAACAAAATTAGGGAACACTCGTGATTTGCGACCTAAGACAAAAGAGACATCAAAGTTCAAAAAACACTACTTACATATCAAGTTAAGTTATGGATTACAAGATCTTCGTATTTACAATGAAAATTCATATTGCATATGAAAAGTAGATTATGCATTTCAGTTAT S12853 349ATGACATATCTCTTTTTGTTTTTTCAAATGTTAAATTAATATTGAGGTGCTTATATTTGGCAATTTTGAATTAAGTCTGAATATTTTAAAAATTTGTGATTGAGACAATGTTATAATATTTTTAACGTGCTCTAACTATTAATTTTCCTTTTTTTTTCCGCGATCAACTATTTTAATTTCCAATAGTATGCTACCCGTGTRTATACACAGGTTATCTAAGAATTGAGATCTGCTAGAAATGCAAAGCAATTAGGGATCGTGTACAAGATATATTAAACATTTTACCAACTAACCATAGAATCTTTTTCATCAACACGACTAGATATTTTTAAAAGAAATCAACACAAGTATTTAAGCAAGTTTTGATTTGAAAATTCTGCATAATCCCCCAAAAGGAAAAG S03246 350aACTTTTTATGATTGACTTGGTTCTCAAATTCCGACGGTATTGAGTTAAGGAATTTTAATGGTGCCTATGCTATCRGTTTTGGAATAACGATTATGAGGTTTGGATGAATATTTGGAGTTGCATAAATACGTTGCTACAAAGGTTTATTTTTCTCTTCTGGTAGTAATATGGAATAACAGGTTACAACCTATTGATTTAATATTAATATAATAGGGGAGGAGTGTATTTTTTGAAACAGAATATTTTTGGAAATCGGGCACTGCCTCCTAGACGTTAAGACTGAAATCTACAGTTTTGGGCTTATATTGGGTTTGCTTTTATTACTATTGGGCTGCATACATACAATATAGTTATTTTAATTAATTTTCTTTATGCTCTAACACTTTGGTTGGCAGGGTACAATTTGCAGCTCATGGT S12962 351TGCAATGGTCAGACTACTCAACACAACTCTTGTTGACTTATTGTTCTTTAAATTTCTAATTTCTTTCTTCCAAAAATGATTTTGAGAGGATGAATAGAATAAAATTCTTAGAAGCTTCCTTCCTGCAAGCTGAGGAAGATTACTTACTAGGAGTGATAACTTGGTGCACCACTGCAATTAGTTTGATCCATGTGGAGACCRTTCAAAAAAATTTACATTGATTTCTCTAGATGCATCATGGATCGCAATTCAAAACTAAACTTTACCCTTCCATGGCAATGACTTCCCTACCTTATTGAGGAACTCCACTTTTTTTATTACAGAAGAAGTGGCTCAAGGAATTTTTGTGTAACTTACAAAATAAGTAAGTGCTAAAGAACCAAAGACTCTTGGCAGCTTAA S00144 352TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGAAAATATCCACTCATTATTATTTCCAACATGAAACGCTTGTTCCACATATTCAACAAACCATTTTATTTTCTTTTTTCAAGAAGAAAGAAACTTCCAAACATGCATCAATTTTATTGTACTAATCTCTCCCTTGCCTTGAGCTTACAGGAACATTGTTACAATTGGTGTTCTGCTTGCTCATGATAAAACCCAAATCAACACCACATAATTTAGGAAGTGAATTGGCCTTGTTTTCGAGCAAGGAAGGAAGGCGAGTTGCTACGTCGAAAAAGCACTTACATGCAGCCATTCGTTGAATTTGTGTTGGTGCTGATGCTTTCACTGCATTAACACTTTGGCAACAAACACCTGAAGGGGCACCATCATCTCCACCAATCATGTAATCTACGCACGAAACTAACAGGTTATASACTTGTGAACAATTGTAGTCATTTGATGCTGAATTTGTTTTAACTGGTAGTCGTGCCTCTGAAGCTTTCGCTGTAAGAACAAATACAACTAGCACAGCTAAAAATGTGACAAACACTTTCTTCATTTTGTGAAATTGAAGCTAGTTTCTATATATCTCAATCAACTTTTTAGGATTTGCTTGTGTTTTGCCGCGTGGGTCGACCAGGGTATTCCGGACCGGTACCTGCAGGCGTACCAGCT TTCCCT S08166 353ATGAGTTCCGTATGAAAAATATACTGTTCTGGATGAATTGTGGCACGAACCATACATCCATGTATATATATCCTAATACTGTCCTACCGTCCACTTACAATGATTGTGCAAAGTTCTTCAATGAGAAAATAAGTCCTAAAAACGGTAGAGCTTAATGACAACAAAGAAAATAACCAATGCGTTACCATATTGGCAACTATAACTAAATGTGAGTGCATGTCATTCCAAATTACGCATTTCTGCGTTATTCACGAGATTATTCATACTCTGGGAGTCACAGCACCTCCCATTGAATTCCACACGACATTTGACAATGGATGCCACCCGGAAGAGGGCTGCATAAAGTCTCCTGAGATTACAAACGAGAGATCTGGAGGGGTATCACTGAAACATCTCCCACYGGCGGGAACAAATCTAGCTCCCCATAACGCTCCAGGACACGCATCCTGCAGTCCTCAGCAGCCATCATTCCAGTAGAGTATGCACCATGCACAGACCCCGTATACAACATACTTGTTGCTTCCCCTGCAAAGAATAAATTGTCTACAGGAACCCGTAGCTTCTCATACAGATCATGTGGTTTCCCAACTGCATCATAGCTATAGGAACCTAGTGTATTAATATCTGTACCCCATCGAGACACAAGATACTGAATCTGCATGATTGAAACAAATTGCATCTTCAAAACACCAACAACATACTAGTCACTGAAAAACAACTTATTAAATTCAATCATATAGCGATTGAACTAAAATGAATAAAACTTAGGACTTTAGGAGTCTGCCACTTATAAAA ATATGG S01081 354ACGTACTTtcnTTTTCTTTTTATTATTAATTCTAACAGCTTTAGCCTTCAACCATTTTTTATGGTTTGTTCAACCATGMCTTTCCGTTCCTTGAGACTGGTTTAAACTTGTGGTCAAAAGCCTTTTTTGCTGCTGCTGCTTCTTGGACACAACATGGGTGTGATACAAAATGATATTAGGCTTCATATCGAAGTACCTTATAAAATGATCTGCTGTTGCATCTTGTACCTGTTGATCTTGAAKAAGATCTTTAATTGCTTCAGGCATRGGTTSGTCATTCATCATTTTCTTCCAATAATCCCCCAGGTCTTTTCTTGCATGGCTTAAGTTGATGTTGGCAACCTATTTATTAGTAGAGATAACATAGAAAASTCATAAACCATAATTAGCACAAACTCAATGGTTCAAATTTTAAAACAAATRAGTTRCTACTGAAAAGCTTACCAGGAGAAGMGAMAAGACTAMGAASAAGGCAAAGRTCAKGGTCATAGCYKKT S02183 355gaccnntgctTACATCCAGTCCCCAMRWMMCSYnntYRGGAGWTnCAntWKSKRKCnAATCnnnnaCAnWTTnTGAAAnncnnTnnnTnnnTACCATGGGAGGACCTTGATGATGTCGGATCACCATACCCCCACTTTGCTTTTCAAACRAAGTATTATGAGGAACATCTTTCTCAYCTAAAAACATAATTCTATGTTCAAAAACAAATATACAAGGCATAAAAGTACRTGTATCCAAAAKTAGCATGAATAAAAACTCGATACCTTGGGGTTGATTAGAAGGAATCAAAGTAGTCGACTTCTCCACGTGCTTGTCATTAACATCAACATTAGTGATCGACTTCTCATCGTTATKTGGTTGGATCACATCAACATTCCTACCCTTAGTAGCAGGCTCGYAGTAGTTTTGGACTRRGCTTGTTYAGTTTTGTCACTTTGTTGGCCAACCTCTRTAGCAACTCTTTTCCTTTTCTTTGGCTTCACTAGGTCGGCAAAGTGTTGGTGGTATGCTAnGATTATGAGATTTCGACATGGAAGCCCAAACCTTCCTGAAAT S00350 356TGggttgtttggtgagaacgaTAAGTTTGCCACAGGAACAGAGGTAAGAATAATAAAATAATAAATCATCCATTGCTTTTGAAAGATTTTGCAAGACTGTCTCACTGTAAAGTACTTCCAGTCCAAATATTGGATTCTTCTTTATAAGCCTGGTTACATCACTTGTACTCAAGTCTTCAGATTTGGGCCATTATTCATGGATCAAACTGTGAAAAAAAAGTTAAACAAAATTTATTTACAATTGAAAATCAGTTATCTTCCTTTTAATTTGCCCAATGTGAGAGAAATGCATTAGAGTCTTTSACAATCTACAATGGGAAGTTTCATGCTGGGACTAACATAGGACGACAATTTTTATCTATTTTCTTTTACTTATTTCATGCTTCTGTTGTAGGTTAGAAAAYGATACTGCCATAGTGGTATTAGTATAATATAATATACTACATCTGYTTTAGAAAAAGATATGCATTTATCTGAAACTATATCATGCATATGTTAAACTCTGAGAAGCTCTTTGATAGATGTGCAACTGTAAAACTTCAGAGCATTACATGCACTAATGAAAAGCTCTTTGATGCTTTAAAATCTGATACTTGAAACTTCTATAAAATTTGATGTACTTGATCACTAGTAACTGAAGACTCTACCCTTTTTGTGCACAGGCTATAGCCAAGAAACTGGCAGAGCTGAGTGGGAAGGGAGTGACAACCATCATTGGAGGAGGTGACTCCGTTGCCGCTGTGGAGAAGGTTGGACTTGCAGACAAGATGAGCCACATCTCCACTGGTGGTGGTGCCAGCTTAGAGCTTCTTGAGGGAAAGCAACTCCCTGGTGTCCTTGCTCTTGATGATGCTTGAGCAAAAATCATTCGTTCCTTTGAAGTTTGTGCTTTATATTATTATTATGGTTGGGTTTCAGCCAACAGTGGATTAAGGTACAATGAGAGCTGCGAagttctTgcTCCctgaaaGGCTTAA S02074 357ATGGanTTCTAAAAGAATGCCTTGTATGTGACGCGTACCATTCTAATCCTAaCTATATTTCTTTATATTCCTTATTTCACAAAAAGACACATTACAATGTGTGCCCTGTGAGGGAAATATTGTAAATGTTAACARCGCAAGAGTAGTTTACACAACCTCAAGATATCAAGGAAGGTATTAGTGTGTAATTTTGCTCATTTTTTTAAGAGACAACAAAATTTTATTCTCATATACTTATCAAAGCCACAAGATGTGACCTAAATATATAAGCCAAACATTACAGAAATTATTTTTTGCCATATGGTTGCAGCACCAAATTAACATCATCCCTAAACACAAGAAAATTTGAACACTAAATCCATCTAGAAAGCCTTCKTAAACATAGTTTTTCTAGGCTTAGAAACCACAATCCTAGAATCAAATAAACATAAAGACTCCAACCATAGTGTAATTTTGCTCATTTTTATTTTGATACAAAGTGCTAGGACATTAAAACATATTCTTTCTCTAATGAAACCTCCTCTAAAAAACTAGYCGGAGAATCCCACCAACAGAACCATGTGTCATGGT S03991 358agcttatYCCCCaaGAcgCTGTCAGCCATGTCGATTTCATTGTCAAACWAGGATCTCCTCCCTATGAAGTTCCACTCCCAACCTACATCTGTGTGACTCCCTATGTGCTGAATTAGCTGTTTTTGCTGGCAGGAAATGTGATATAGCTTAGGATATTTTGTTATTAGTGGAGCATCATTAGCAATTCCATTTTGAAAGACATTGCCCTGTTGCGATTGGTGGAACACCGCCTTTAGGTCCTGCCACCATAAAGATTCATTGTTGCCTCTTGTTACGTCATCCATGCACCTCCAGCCACCATATTTTGAATCCAATATTCTGGCCCATAGTTCCCCTKGGTGCTGAAATARAWCCSATCTCCATCTTCCAAGCAGTGCTAGAKTGRAGGTGTTGATGTCcttcatgctctaacacatacctgttt ccatcc S04785 359ATTCAGTGATTTTACCTGTTTGCTTGCGAGATTCAGGAGGAGGGGCCCCATATTGACGAGGCAAGAAAACCCCYGTTCCAGCGCAACCCCTTTTAGTAACACCGGATCCACCTTGCAACCCGGGTCGCGACCCGGATCCGAAATAAGGCACCTGTTGGGTATTCTGGTYCTTCACTTGAAGAGGGTGCCATGCARAGTGAGGCAAAACGTGCGTGCAWTTCACAGCTTCATAGTCATACC S02874 360GTATTATGCAGCTATGGTCAAGACATACTCATACTAGCAAAACAGCATTAATTTGATGATTTGACTCATGGCTCATTTCCCTTGTTTAAATATAGCCATGTGGAAGTTCACTTTGTTATGGATTCCAYTTTCCTATTCATGTGAGGGATTTGGTAATTKGTGAGGCACGACCAAGGAGAAGGGAAAATAAAAAAGGTGCAAGACCATGCTAAAAAGGCTAGAAGAAACTATAAATCCTGATATTGTTGTTGAGAAAGAAGTGGTTTGATTTGTGATAAATAAATGATAATATCTCACACAACCGGCCWGCTTCATCTTACCCACACAGTTATTTCATAAACTTTAGAAGAWAACGTAAACTTATAGTAGTTGATTAGAAAATTAACAGTTGAAATTGTGATTAAATACATTCACATATGTTCGAAAATATAGAATTGTTATCCACTAACGTGTATCAAGCTCTTTTTGCGGGATCTT GCATGGTCATAGCYKKTTS04348 361 KHVKWYWHAAYYWRATGARMAGKGMATRKGRTAACWKRSMKWSCAgAgnnnnnGAGACTAGAACCATTAACATTAGCCAGAGCCACAAAAGGTCTAATAAAAACATATCATGAAAATAATTTTCTAAAAAGAGCAGCAAAAGACCTGTGCCATCACAGTTGTAGGAATCTGAATAAAATTAACACCACGTAGGAAGGCAGAGGCAGCAAAGCCACACATGTCGCCAATCACACCACCACCAAGAGCAACAAAYGTACACCGCCGGTCGAGCCGCGACTCGATGGCCTTGTCAAAGACTTTCATAAGAGTATCCTATCAGTTGAACACACAAAGACTTTCTTATGCAATTCTCAAGAGTGCCAACAAACACCACAGCCAATTCAAAACACATGAGACCTACCATGTCCTTGTACTGCTCACCATCAGGTAAAATTACACTCTCCACAGAAACATTCGGGTTTCCCCTTGTCAAAGCATCAACAACCTTGTCTAGATAAAGTGGCGCAACGGTTTCGTTAGTTACAACTAGGACTCTCTTTCCATGCACATGCCTATTCCAATAGTGAGAACAGAGCACTTCAGAATAAATATTAAACAAGAAATAAAATCCATGCCTTGTTAGAAACTTTAATTGAATTGAACTTCTCCCACATACYATTAAATTTTATAGAAGCTCTTTCATTTAAAGTCTCCAAAAGTTGAGGCACATATGTTGATTTTAGCTTAGAGGAGACTTCAATTC ATTCTATCTTCTS01209 362 AATACTAAGCTGAAGGAATCGATTGCAAAATAATAACCCTTAGAAAACACTACGGCTTTGTAAATCATAAACCCTAAGCTCTCTCGCCCCTAATCCTACGAGCTAGCTGAATGTCCTTGGGCATAATGGTAACCCTCTTAGCATGAATAGCGCAGAGGTTGGTATCCTCAAAGAGCCCAACGAGGTAGGCCTCAGCGGCTTCCTGAAGAGCGGAGACAGCRCTGCTCTGGAAGCGTAGATCGGTCTTGAAGTCYTGAGCGATTTCCCTTACGAGCCTCTGGAAAGGAAGCTTCCTTATGAGAAGCTCCGTGCTCTTCTGGTACTTCCGAATCTCCCTCAGAGCCACTGTCCCCGGCCTGAAACGGTGGGGCTTCTTCACGCCGCCCGTCGCCGGAGCGGACTTRCSTGCTGCCTTGGTGGCGAGCTGCTTCCTTGGAGCTTTTCCTCCATGGTCATAGCTGTTT S01999 363CaMCGGCGATTAAGCAGCCATATTTncTGGTCAACACCAAGMnWGTCTTAAGTTCCCTTCAGCTACTCTTTGGTCTAATTTTGATAGGAACCTGTCTCAGACCAAGCCTAAGGTTTAATTCCATAGGCCCAAAAGGGCAAATGCGTCCTAGGTGAAAAGAAGTTAGTTAGAGATGAGACAGTGTGAGTGAGGGGTCTGTTATATGGGAGGGGGTGAGGCTTGTAMGGGGTATGGATGAATTTGGAATGTGAATTGGAGTCTAGAGATTCTTCTCCGACTTTGGGGAGCACTTGCTCTCACTTCTTTCTGTGTGTTTTCTGTTTTCAGCTTGTTTTTCTAATTCTGCAGCTTCCCTCTGATACAATATGTATCATTGGTGCTTTCATTGAGAGATTTGTTCCAATCASCATATGCAAACGAGGATGACGTCCTGCCTYGATGCTGTTGAATAAAAAAWMTCTACCATCGACTTCMTCCTTMAAWCWCATCWYCAAYMAMTTMAKYWACATTCCDYYCMCATGGTCAWAGSH DKT S02112 364CCATAGATCTGAAACAGAGATCACAAGGTTAACGCTTTTATTCtccaTTGGATGTTACCCCAAACACCCCGYACCTATAATCTAGCACCAATCCAACCCGTTTTCACTCGGATCTAGGACCTCAGGTAATCCCCCATGAATTTTCAATTATTATCAATGCTTTTTCAACTTTAGTTTATTAATTCAGCYAGGGTTTAGTGTCTAAGTGAATAAGGTTGGGATTTGYGATGGCTCCGACRATGRTCCGGAAGGTGATTGAGGTGGTGAAGGACCAGACCARCATAGGAATAGTCAAGGTCGCGAGCAACATGGCGTCGGAGATGGAGGTCACGATTGTGAAGGCGATGAGCCACGAAGATGACCCTGYCAGTGACAAGTACATAAGARAGATCTTGAACCTCATGTCTCACTCRYRCGRCTACATCCACACATGTGTCACCGCCATGTCCAAGCGATTGGGTAAGATGCRCGAATGGATTGTGTCGCTCAAGGCRCTGATGCTCGTGAACAGGCTCATG S03252 365GtAGCATAACTGAaAATATAAATTCCCAATGCTCCTATTCTTCAAGAAGCAATTCAAACTATAAGACAAGTTATATGACCTTCAAAAGTGTGCCCATAGAAAGTGTGTTTTTAAGGTTTTTCGTTGTCCTGGTAATAATTTAACTAACTAGATGGCTTGTAGTACTGTCAGAACATGTTCTCACTTGTTAAATTTCTATTTTGTGGTACGGTCCCAGCTCAAAGATGTTTGCTTTATACAAATTACGCGTTACAAATTAAAGCATGTTAAACAAGGTTTATGAGAGAGGAAGTTTTGACGTRATTCAAAGCCAAACCAATAAGTGGTTAGACATGTATTTATAATAGAACATAGATTTACCATAACAGCCATAGATTAATATTCCAAGCTAATTAAGTGGTTGACAACCCCGACAATACCAATATATACTGAAATTCCTGATTACACGCCCTCTCTCCAACGTGTTGCTGAATTKTCAAGAGGCTTTCCTATGTGGCTGGATATATTGCATCACACAACATCTGGGCACC AT S04937 366gaatgcttgtttcacgtaagcttcttgactttaTCRTTCTCTCCCCCGCCCCCCAAATACCACWAAAATTCCGAACGCTGTCATATTGCAATCTAATTGTTTAATACCCAAATCCTTCCCTAGCTCTTTTCCAGTATCTTGAGCTTGTAATCTTCCATCTTAAAAGCATACTGACTGATGCAATCTTCTGATTAATTTAGACCTGCATCAGTTACTTGCTTGCAAGTTGTAGAATCTCTTATTTTYCTTTTCACTTCACTGGTTTGCATGTCCATACAATTCGAACTATTTTTTATCTTTCAAAGATTGGAATGACATTAACTTGGTTTTTGATCCTAATAGATAAGTCATATCAATTTAGTTCTTGAAAGTTGGAGACTRAATGTCCTCTAAATAAATTGACATCAATGTAGATCCTCAATAATAGAAAGATGACATCAATTTASTCCCTAAATCTTGCRGTTTGTGCATAGAAGGATGGTTTTTTGGTTACTTTCCACGGTTGAGGTWCTAAAYTGATGCAATATCTCTTAKGGAGTTARRRVMMAAAGTGATGTCTACCGAACCTTCCAAGGAACTGGCC GWMgTTT S04938 367aMMAKYTATGACCATKCGAACCTTCCAASSMCCAAAAKGRAWTTTCACTCYWAAATWTATGTSCACTCCTGACTGCTTTTACATTTAGTGTYTTCATTTCATTGGGTTTCRTCTATCAGAATTCAGTGATAAGAAACAGTGCTTCAACAATAGGTTGTGGAACATGTTTTTYTGAGAGGTAAGGTAGTCACAATGAAAAAAAGGACAAAACTTAGATCCAAAGCTATGTTGCATTGATTAACAAAGTAATCACATAATTTTGGTGTCATTTTCTAATAAGAATTGGAGTTTCATCTTGAAAGTTTATGTTGACCTGTAATGCAAACCTGTATTGCATAGATTAGTGAAGTAAAACTTTGTTTTTTATTAGAGAATAACATCAAAAGCATTTATGGATCTGCATGAGTTTTKTCCTAAAAAGGTGTGAAATAGGGGGAAAAAAGCCACACTGGATGTCAAAACCATTGTTCATCTGGTATATATTTTCATCTCCWTATGATARTTTTTTTTTCTTTTCTGATTTCTTGTGAAATATATTAATTAACTKCCTTCTTTTACAKGTAAATGAGAATGTTGTTAATTAATATGTTAACCTAAACSATATCTTTAATGYGTTKYCATYTTCTWTTCGTTTTG CAGTGATGGTATCCS06786 368 STATTGCACSCGCTTTTCGTCCCGGTCAAGAAAAGATGGTTTATGTGTATCAGCTCTTGGCAACAGGCACATTGGAGGAAGATAAGTACATAAGAACCACTTGGAAAGAGTGGGTTACTAGCATGATTTTTAGTGAGGCTTTTGAGGAGAACCCTTCACACTCGCGAGCATAGAACATTGAAGATGATMTACTGAGGGAAATGGTTGAGGAGGACACGTCTAAAGCAATTCATATGATTCTAAAGAATGAAAAGGCTTCAAYAAATTGAAGAGAGGTAATTACGCTTTTTTCATATGAAAACATGTGCTTAATTTATGTTTATATATCTTAATCCTACATTCTCCCTATTAGTGTTATTTACAGTGTTTGCACTAGATCACTAGAATGCTTGTTGGCATTCACCTTCAGTGTTGGAGACAGATTTGACACTTGTCGTCTCGAATGCCAGGGCAAGTTCGAGTTTAGTAGAAACTTATCATCCAAAATTAAAATTGAAAGCACTAATACAAAATGCACAATTTGAAGCCATTCATGTCCTCTCTTGGTCTGAGTCTTGTCATTTTGTGGATTGAATTCATGGTTTCTCTTATCCGGTGACATTGTTRMCAAGTAATACTACTATAAATTCAGATTTGGATATCAGATAACCATGGTCATTAATAGTAATACTAACATACTATACATATAATACCTTACAGGACCTTGTCCGAAACTTGAAACAGGATCAGGGACAGCGAAAAACAAACATGGTCAWAnCYKKTTYY S06787 369TTACAAATAGGRRAAAACTTAGATATACATAGTTCTTTAAGTTTGATTACATTACAAATAGGAGAAAACTTAAAYATRCATAGTTCTTTAAGTGTTGTGTGTGCTGTTCCATAATTAGAATTGGAGTTTTACTTACCTTAGTAATATGTATAATTCTAATTGGAGAACAGTACAAACAAAAACACCTAAKGAACAATACCTTAGTTTTAATCATATTTGTTTTGTTCATATAGCTTATCAATAAGTGAAGTATTTTCTTGTTCATCTTGATGCAGGTGGTGGAACTGAAACCTTCATTGATTGGCCAACAAGGATGAAAATAGCACAGGACATGRCTCGTGGCTTGTTTTGTCTTCATTCCCTGGAGAACATTATACATGGGAACCTCACATCCAGCAATGTGTTGCTTGATGAGAACACAAATGCTAAAATTGCAGATTTTGGTCTTTCTCGGTTGATGTCAACTGCTGCTAACTCCAACGTGATAGCTACTGCTGGAGCATTGGGATACCGGGCACCAGAGCTCTCAAAGCTCAAGAAAGCAAACACTAAAACTGATATATACAGTCTTGGTGTTATCTTGTTAGAACTCCTAACTAGGAAGTCACCTGGGGTGTCTATCATGGYCAWAGCTKK T S06803 370ttgcgtaatctttctgttctgattttgagtaggaaccaatttagtggacatattccttcaagcattgcaaacatttccatgcttaggcagcttgatttgtcactgaataatctcagtggagaaattccagtctcctttgaaagtcaacgtagtcttgatttcttcaatgtttcttacaatagcctttcaggttctgttccacctctacttgccaagaaatttaactcaagctcatttgtgggaaatattcaactatgtgggtatagcccttcaaccccatgtctttcacaagctccatcacaaggagtcattgccccaactccagaagtactgtcagaacagcaccatcgtaggaacctcagtaccaaagacataattctcatagtagcaggagttctcctagtagtcctgattatactttgttgcatcctgcttttctgcttgatcagaaagagatcaacatcgaaggctgagaacggacaagccacggggagagcagccRctggaaggacagaaaaaggagtccctccagtttctgctggtgatgttgaagcaggtggggaggctggagggaaactagtccattttgatggaccattggcttttacagccgatgatctcttgtgtgcaactgctgagatcatgggaaagagccatggtcatagcctgt S06804 371tttgtttctcttatgtatgtggagtcttgttgtgctcccttcatgcgtgagaccagctttgtgtgaagatgaaagttgggacggagtggttgtgacagcatcaaacctcttagcacttcaagctttcaagcaagagttggtggacccagaagggttcttgcggagctggaacgacagtggctatggtgcttgttcaggaggttgggttggaatcaagtgtgctcagggacaggttatcgtgatccagcttccttggaagggtttgaagggtcgaatcactgacaaaattggccaacttcaaggccttaggaagcttagtcttcatgataaccaaattggtggttcaatcccttcaactttgggacttcttcccaaccttagaggggttcagttattcaacaataggttaactggttccatcccttcttctttaggtttctgtcctttgcttcagtctcttgacctcagcaacaacttgctcacMggagcaatcccttatagccttgccaattccaccaagctttattggcttaacttgagtttcaactccttctctggtactttaccaactagcctaactcactcattttctctcactttcctttctcttcaaaataataatctttctggcaaccttcctaactcttggggtgggagtcccaagagtggcttctttaggcatggtcata gctgtt S06788 372gTATTTGATTAGTTAAACCGCAACGCGGAATCTCTTTTCTCGAACTGGCTAACTCTCAGGCAAGTGGTTCGGACGCTGATTCCAGCAACAAGCGGCTGGTGCTCGCACTGTATGACGCCCTAAACTCCGGCGACTCCGACGCCGTCGTCAAGATCGTCGCCGCCGACCTCGAGTGGTGGTTCCATGGTCCGCCCTCACACCAGTTTTTGATGCGCATGCTCACCGGCGACTCCGCTGCCGACAACTCCTTCCGCTTCCTTCCGCAGTCCATCGCCGCCTTCGGCTCCACCGTCATCGTCGAGGGCTGCGACACCGCCCGCAACATTGCCTGGGTCCACGCCTGCACCGTCACGGATGGGATAATTACTCAGATCAGAGAGTACTTCAACACCGCCCTCACCGTCACCCGCATCCACGATTCCGGCGAGATTGTTCCGGCTAGCTCCGGCGCCGGCCGTTTGCCCCTGTGTCTGGGAAAGCAGCGTCTCCGGTCGGGTCGGGAAATCCGTACCCGGTTTGGTTCTTGCAATATAAAATAATTATTAACAAGTAATTAGGGAAGAACGCGGTCACGTGTGAATAATAATTAAATAAGGAGGTTGTGCACGTGGCGGTGACTGGGTCGAACGGTTTCAGGGAACATTGATATATTTTCGTAGTATTGGTGTGTTCTRGAGGTTAGAGAGATGTGAGACCCTATTGGTGGGGTTTCTTATTTCTTTAATTTTCTCAGGTTTGGTTTGTTTTTGTTTTGTTTGCTTGTGTGTTTTGGGCATGGTCATAGCCKK S06805 373TATTTTAATTAAGAAAATAAAGGAGTTTGTTTATGCTGCAATTTATGATCTAGATCCAATATAGGGAAGATGAATGCTAGTAAGGCACTATTTATTGGGTAAAATCCATGTGGGTCCCAATCCATATTTACTAGTTCTCACTCCGTACTTAGTGTAACTTACATGTGTCATCCGATTATGGAGTGTTGTGCTAGCATTTCTCTTATATAGGGAATTAGGGATACAAAATGGCTTTCCCTACTTTTCGTGGGCAACCCCAATTTGATAACTTGGCCACTTTATGGCTAGACTTCAGCCTAATTTATGTACTAGATATAGTATATGAATTTATACATAACTTCACATGCCCTGAAATTTTCCACTTGATTTGCAGGCAATTGTGACAGAAGAGGATGGAATGGAGTCAATAGCTCATAGATTTCTTTCTGCTGCTGTCAAGGTAGAGTTCCATCCACCTGATTCTATTTTTGATGAAATGTTTCTGGCTTGAAATTATTACTATATTTATTATTGTATTTTAACACTTGYCTTTACAACATGTAGTATAATACTATAATTACACTCATGCAAGTTTCCAGGTCCATCTTTACAAAATTGTAAATACTAACACTGCAGRAATTTGGAAAGTTATAGTAGTAGTCGTCTACCATCTACGGccAAAMCMWKGKYMWWRSYBKKt S06789 374ggSttYcccaaaTAggtcagcctctccataaaccctcaagagcgtattatagctaatgacgttgggttgaatccccattttcctcatgctccagaagaggcggtcggcttccttgggcatgtgaagctggccataaacatcaatcatgatgttacaagtggtgagatcaagagggcatttagcttcattcatttcggaRaatagagaaagtgcttcaacaaacttttggttgtcaacgtagatggcaagaagggtggaatagctgacggtgtcgggttgaacggcattgtctctcatctcttgaagaagaaggcgagcctcacggaagagcttggcttttccaaagacattgatcatggagttataagcaataaggtcgggggtaatagtggaggctttcAatctggagaaGatagaaatggccttggaataatcGgacaacttgcgggcaaggtcaatcaagttactgtagagaacgaggtcgccggagacGttgtcttgctccatctgctggagccaaaagagggaagaatcAaacaagccgtgtttgccgaaacaagtaattagggtggagtaagtgtacctatcgggggagaggcccttttggcGcattTcATcGaacaggccgtgtgcgaggtgccactgcttggcccGaaggacgttgcggagaaGgACGTgGTgGGCGaMGWKGSRGRRAMRRWMGWKgBMCKYSWMSWKKRWSSVWBGDYMKAGSBBBttBYMnWtgatccMtggtcatagcYKKtt S06790 375gWcWMKWWTTKGCAMASRMKCVARGCTCGACMCTGKTCTATAATCTTACCCCTGATAGAACCTTCAAGTTCAGGCCTTGGAGCTCCGGTGAAAGTGAACAAGTATGGCCGCTTTTGATGTCTGATTTTTCTCTGCCACCGGTAAACATGAGTGTCCTCTGATGGGTGGAAAGAAGTTGGGTACGGAATTGCGTAGTCATTATTCCACGAACTTGCTTCAACTGCTAACATGGACATGTTCATGGATTCGGGTATAAACCTGAACTTACTACCCCAATAGGACGCATCATCATATTGTCTCCTGAAATCCCAAGCAATCCTCCCAGAAACAAGGAAATGATCTCTGCCCCACATTTKCTTCCACTCGGGTCTTTTTGCGACCCATTGAAGAAGATCACGACCAGAGGAATCTCTCTCTGTGAGATTAGAGAGCCAAAGGAAACGGCTAACATCAAGACCAGCATAGAATGGGACGAAAATTGCAGAGGCGAGGGAGGAATCGTTGGTCAAGCAGCCATATTTGGTCATCCTGTTGTGAAAAATAACTTCCAACAAGAACTGGTTGGTGGCATAGCAAGTGTTGTTGGAGAAAAGCCCTTGGGAGTAGGTAATGTGAGGACCTAAACCATTGTTTTGCATGTATGGACACATGTTGGGTTTGTCAGTGCCTCTAGTGAGGGACTGGCAATTCTGAAGCAAGTAATCgTTnAAGCGGGAGCATGGTCATAGCBKKTTT S06791 376tACBTAATTTTAAGTAGGTTGAAATGTYTCTTACCCTTTGTATGAGATCTCTGTTTGATTCACCTAGAAAGTGTTCCTTCACAAGTGACATATATAATTGAATCGGTGAGCAAGGGAAACATGCGGAAGATCAAYAGCAGTTAAACATTGAYMAAAGAAAGAAAGSATAATTGACCTCATACCTTWCGTTGTAGATCAGAAAGCTGATCCAGCATGAATTGGGTCTGCATATATAGAATGCTATGAGAAAAGTTGATATAGACCATTGACCATTGAGATTATATATGAAGTTATGAGAAAGATCAACTAATTTCTTCTATTCTTTATTGCACAGCTAAAAAAAAAATGATTATATATGTCAAAATGGAAATTGGCAACGTTGGAAACTTTAGTACCCTTATTGATCTGATTTGTTTCAAAGACGAATCTAGCTGCCTTTCAAGTGACTCAAGCTCTTTGCTGCTTAGAGGACCAAGATCTTCTCCCATAAGGTTCCTAATGAGTATCGACCAGTCAAATATATATTAATAACTCATCAGTTCGTATTATGTAGCTAGCATATACTTCTAGACATAGTCGAGTCTAGCTCTTTACCTTTGAGAACGCTGAAGAGCTTCATAACGCGCTTTCAGCCTCAAGTATTCTTCATGGTCATAGCYKKTT S06792 377KWRTWAACTTCnaTTCCWTATCRTCTCTATGATCARYATSRGCATAAGTTTCAGAAGAAGTAATTGGAGAGTTGTCTTCAACCAAAAGTTTCCCTTCCTTAGCTGCAACGAACASGTCCTGAATAGGACCATACAAGGCATTGTGATTTGTTCTGTTAGGTGGCTGCGGAAAATCAGTCAAACTCTCCCTTATCAAACTACATTGTTTCTCTATGCTTAATGCCCCAGGAATAAAATAAAAGCCTGCAAATTAAGTATCACCAAGTGTGCTTGAGTTCATTAGTTACAAATGCACTTATGATTAGTTTCTAATCACTAATTAATTATCCCAGTCAAGTACAATTCAAGCCATTTGTTTCAAGTTACTAAGATAAACGGCAAATAAAAGAAAAAAGAAAATACCTGGGCGATTTTGTAAAGCAAAAACCGGAGAGGTGAACTTGTCGTGAAGAACGATAACACCCGAAGGAAGCACAGCGTTTTGGTGATAGCATTCTAGAATAGATCTAAAGTCAAGGACCTCCGCTAAGTCCACGGGTTTAGGTTGTTTTTTCCTGTTAAGAAAGGGAATTTCAATTASAATTTGCAGAGATTACAACTGAAACAATCTACGTTCAAAGGAAATGAAATAGTAAAATACTTTTTGTTCTTGGAAGAAGCATTGTAGTCSTAGTAGAGCTTGTACTTCTTCTCTGCATGGTCAWAGCSKKTT

TABLE 8 Non-limiting Examples of Amplicons Comprisingthe Various Marker Loci Provided Herein. Linkage Amplicon Group PrimerPrimer SEQ ID Amplicon Sequence Amplicon Locus (cm) 1 2 NO (R/S)[Res/Sus] Size (bp) S04196-1 B1 141527 141528 111/112GCCATCCTAGCTAGCCCTGTATA 236/243 (Gm11) TTTTGATTANNTTNATGGGAAGA (R/S)AAAAATTAAATATTTTTATTTAA TTGAAGAGTAAGTTAATTTTATG AAAACAAAAATTTAACATTTTCTTACTTATCTTTTAATTCAAATTT TATTTTATTTTCTCTTATTCCAA CAATAATTCCTAAAGATA[*******/CATGCAA]GTCCAA TATGTTTAACTCATCACATTTAA TTTCATTACGAAATAATCAACAGGTCAA S04938-1 B1 S04938-F1 S04938-R1 113/114 TGTGCACTCCTGACTGCTTTTAC101 (Gm11) ATTTAGTGTCTTCATTTCATTGG GTTTC[C/T]TCTATCAGAATTCAGTGATAAGAAACAGTGCTTCAA CAATAGGTTGTGG S04937-1 B1 148638 148639 115/116TCAATTTAGTTCTTGAAAGTTGG 224 (Gm11) AGACTRAATGTCCTCTAAATAAATTGACATCAATGTAGATCCTCAA TAATAGAAAGATGACATCAATTT ASTCCCTAAATCTTGC[T/C]GTTTGTGCATAGAAGGATGGTTTTT TGGTTACTTTCCACGGTTGAGGT ACTAAATTGATGCAATATCTCTTAGGGAGTTAGAGGACAAAGTGAT GTCTACCGAACCTTCCAAGGA S08344-1 B1 136830 136831117/118 CGACACCAATTTCTCCATCCTCT 112 (Gm11) CATTGAAAAACAAAATTAATCATCTTA[C/T]TTATTTATTCTCCG AAAATGGTTGATTTACATTGGAA ATCAAAGATGCCAAGTTCCGACAT S08343-1 B1 136886 136887 119/120 GACTTACCAAATGAGTTTGACCA (Gm11)GGTTTTACCCCTCTTGATTGCAA CCTCACGACCATCAACGAGTTTG CCTCTGTACTCAACAACAAAGCCTCCGGTACCAATCTTGTTGTCAA ATGAGAAATTATTGGTGGCTGCT TTAAGTTCAGCGAGGGTGAATAA286 TGGTGCAGCAAAAGCATGCACTG GGGAAGGGGATGATYCCAAATCTGCTTCACTGGCACTACTACTCCT TATGGCACTGTC[C/A]ACTAAT GAAGCAAAACTACGGACACGAGATTCTCCAAAAATGG S08346-1 B1 136886 136887 121/122 TTGTTCTCCCGYTTACACCACAA110 (Gm11) GAATTTGGTTGGGCTGGTTGGAT TTTGTGAA[C/G][A/A]AAAA[G/T]ATGAAAGGCTCTTGGTGT ATGAGTACATGAAGAATGGGRCG TTGTATCA S06786-1 B1144687 144688 123/124 CCACTTGGAAAGAGTGGGTTACT (Gm11)AGCATGATTTTTAGTGAGGCTTT TGAGGAGAACCCTTCACACTCGC GAGCATAGAACATTGAAGATGAT130 [A/C]TACTGAGGGAAATGGTTG AGGAGGACACGTCTAAAGC S06787-1 B1 142755142756 125/126 TGCTGTTCCATAATTAGAATTGG (Gm11) AGTTTTACTTACCTTAGTAATAT175 GTATAATTCTAATTGGAGAACAG TACAAACAAAAACACCTAA [G/T]GAACAATACCTTAGTTTTAATCATATTTGTTTTGTTCATAT AGCTTATCAATAAGTGAAGTATT TTCTTGTTCATCTTGATGCAGGS06803-1 B1 142759 142760 127/128 AACATCGAAGGCTGAGAACGGAC 144 (Gm11)AAGCCACGGGGAGAGCAGCC[A/ G]CTGGAAGGACAGAAAAAGGAG TCCCTCCAGTTTCTGCTGGTGATGTTGAAGCAGGTGGGGAGGCTGG AGGGAAACTAGTCCATTTTGATG GACCATTGGC S04197-1 B1142386 142387 129/130 TGCCTAATGGGAGAGATGAAGAT 200 (Gm11)TAAAGTTATTATTATATACATAA ATATAAAATTGGAAATGAATATT TGTTTTAAATGGAGTATGAAGATCATACCCTATCCAGTATCTACTA CCRGTATCTACTACCAT[C/A]C CTAAACTCGACAAGGCACCTACACTACAATATAAATATAGTAAGGC TTCGAGTAACAGAACCTGCG S07162-1 C1 136849 136850131/132 AATGCAGGGCCAGTTACAATACA 205 (Gm04) TACATACGCATAACCAAAACAGTAACATCAATGGAACAGTAATAGG ACACAAT[C/T]ATTATTATTTT TTTGTTAAGGAAATTTCTAAGAAAAACACAACCATTTGTACAAAAA AGGTATTAATACATAGCTACATG GAAGAAACCTACATTAAAATCCAGTAGTGAGAAAAGATGGGGGCAA TT S07161-1 D2 137370 137374 133/134TGCTTATCTTGTCTGAAAACCACT 156 (Gm17) AATGCTCTCTTCAGTG[A/T]GAATAAAAGGGCTACAAGATATCATAC ATATGCTTTAATATTATATCACTA AATACAATTAAGGATGCTCATCACATTAGGTTAGGTTAGATACAGT TGAATTGCCTTAAAGTCA

TABLE 9 Positions of various markers Linkage SNP Group Genetic PositionLocus (ch) (cM) (bp) S02621 D1b (2) 133.95 51490811 S01519 D1b (2)120.16 48686902 S08177 D1b (2) 131.45 50529112 S00479 D1b (2) 91.6142982998 S02136 D1b (2) 94.75 44096100 S00875 D1b (2) 113.96 47471551S12875 D1b (2) 114.51 47529446 S12950 D1b (2) 114.71 47556177 S12947 D1b(2) 114.78 47576630 S12933 D1b (2) 115.35 47765197 S12853 D1b (2) 116.6848204176 S03246 D1b (2) 117.97 4833665 S12962 D1b (2) 125.66 49371792S00144 D1b (2) 126.03 49461261 S08166 D1b (2) 126.17 49505295 S01081 D1b(2) 132.07 50775206 S02183 E (15) 90.49 49934844 S00350 E (15) 85.4948657373 S02074 L (19) 17.63 2901398 S03991 L (19) 29.32 18029354 S04785B2 (14) 26.08 5096522 S02874 B2 (14) 20.07 3945680 S04348 B1 (11) 37.625916329 S01209 B1 (11) 54.57 9963410 S01999 B1 (11) 63.22 11202391S04937-2 B1 (11) 97.94 36954416 S04937-1 B1 (11) 97.95 36954799 S04938-1B1 (11) 97.95 36954994 S04938-2 B1 (11) 97.95 36955430 S06786-2 B1 (11)99.96 37311026 S06786-3 B1 (11) 99.97 37311730 S06786-1 B1 (11) 99.9737311443 S06787-2 B1 (11) 100.09 37333749 S06787-1 B1 (11) 100.0937333894 S06803 B1 (11) 100.10 37334507 S06804 B1 (11) 100.10 37335483S06788 B1 (11) 100.50 37405385 S06805 B1 (11) 100.99 37492596 S06789 B1(11) 109.51 37923651 S06790 B1 (11) 109.97 38041618 S06791-2 B1 (11)110.26 38197612 S06791-1 B1 (11) 110.26 38197663 S06792 B1 (11) 110.4538279360 S02112 C2 (6) 108.15 45770644 S03252 C2 (6) 102.83 21822996

In another embodiment, the method of detecting comprises DNA sequencingof at least one of the marker loci provided herein. As used herein,“sequencing” refers to sequencing methods for determining the order ofnucleotides in a molecule of DNA. Any DNA sequencing method known in theart can be used in the methods provided herein. Non-limiting examples ofDNA sequencing methods useful in the methods provided herein includeNext Generation Sequencing (NGS) technologies, for example, as describedin Egan, A. N, et al. (2012) American Journal of Botany 99(2):175-185;genotyping by sequencing (GBS) methods, for example, as described inElshire, R. J., et al. (2011) PLoS ONE 6(5):e19379; Molecular InversionProbe (MIP) genotyping, as described, for example, in Hardenbol, P., etal. (2003) Nature Biotechnology 21(6):673-678; or high throughputgenotyping by whole-genome resequencing, as described, for example inHuang, X et al., (2009) Genome Research 19:1068-1076. Each of the abovereferences is incorporated by reference in their entirety herein.

An active variant of any one of SEQ ID NOS: 1-377 can comprise apolynucleotide having at least 75%, 80% 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NOS: 1-377 as longas it is capable of amplifying and/or detecting the marker locus ofinterest. By “fragment” is intended a portion of the polynucleotide. Afragment or portion can comprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, 100, 150, 200, 250, 300,350, 400 contiguous nucleotides of SEQ ID NOS: 1-158 as long as it iscapable of amplifying and/or detecting the marker locus of interest.

Unless otherwise stated, sequence identity/similarity values providedherein refer to the value obtained using GAP Version 10 using thefollowing parameters: % identity and % similarity for a nucleotidesequence using GAP Weight of 50 and Length Weight of 3, and thenwsgapdna.cmp scoring matrix; or any equivalent program thereof. By“equivalent program” is intended any sequence comparison program that,for any two sequences in question, generates an alignment havingidentical nucleotide residue matches and an identical percent sequenceidentity when compared to the corresponding alignment generated by GAPVersion 10.

Traits or markers are considered to be linked if they co-segregate. A1/100 probability of recombination per generation is defined as a mapdistance of 1.0 centiMorgan (1.0 cM). Genetic elements or genes locatedon a single chromosome segment are physically linked. Two loci can belocated in close proximity such that recombination between homologouschromosome pairs does not occur between the two loci during meiosis withhigh frequency, e.g., such that linked loci co-segregate at least about90% of the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,99.5%, 99.75%, or more of the time. Genetic elements located within achromosome segment are also genetically linked, typically within agenetic recombination distance of less than or equal to 50 centimorgans(cM), e.g., about 49, 40, 30, 20, 10, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25cM or less. That is, two genetic elements within a single chromosomesegment undergo recombination during meiosis with each other at afrequency of less than or equal to about 50%, e.g., about 49%, 40%, 30%,20%, 10%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25% or less. Closelylinked markers display a cross over frequency with a given marker ofabout 10% or less (the given marker is within about 10 cM of a closelylinked marker). In specific embodiments, a closely linked marker iswithin 10 cM, 9 cM, 8 cM, 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM or 1 cM ofany given marker disclosed herein. In further embodiments, a markerassociated with one of the markers disclosed herein can be within 75 Kb,60 Kb, 50 Kb, 40 Kb, 30 Kb, 20K, 10 Kb, 5 Kb or less of the disclosedmarker.

Put another way, closely linked loci co-segregate at least about 90% ofthe time. Genetic linkage as evaluated by recombination frequency isimpacted by the chromatin structure of the region comprising the loci.Typically, the region is assumed to have a euchromatin structure duringinitial evaluations. However, some regions, such are regions closer tocentrosomes, have a heterochromatin structure. Without furtherinformation, the predicted physical distance between genetic mappositions is based on the assumption that the region is euchromatic,however if the region comprises heterochromatin the markers may bephysically closer together. With regard to physical position on achromosome, closely linked markers can be separated, for example, byabout 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb;1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 2 Kb, about1 Kb, about 500 nucleotides, about 250 nucleotides, or less.

When referring to the relationship between two genetic elements, such asa genetic element contributing to resistance and a proximal marker,“coupling” phase linkage indicates the state where the “favorable”allele at the resistance locus is physically associated on the samechromosome strand as the “favorable” allele of the respective linkedmarker locus. In coupling phase, both favorable alleles are inheritedtogether by progeny that inherit that chromosome strand. In “repulsion”phase linkage, the “favorable” allele at the locus of interest (e.g., aQTL for resistance) is physically linked with an “unfavorable” allele atthe proximal marker locus, and the two “favorable” alleles are notinherited together (i.e., the two loci are “out of phase” with eachother).

Markers are used to define a specific locus on the soybean genome. Eachmarker is therefore an indicator of a specific segment of DNA, having aunique nucleotide sequence. Map positions provide a measure of therelative positions of particular markers with respect to one another.When a trait is stated to be linked to a given marker it will beunderstood that the actual DNA segment whose sequence affects the traitgenerally co-segregates with the marker. More precise and definitelocalization of a trait can be obtained if markers are identified onboth sides of the trait. By measuring the appearance of the marker(s) inprogeny of crosses, the existence of the trait can be detected byrelatively simple molecular tests without actually evaluating theappearance of the trait itself, which can be difficult andtime-consuming because the actual evaluation of the trait requiresgrowing plants to a stage and/or under environmental conditions wherethe trait can be expressed. Molecular markers have been widely used todetermine genetic composition in soybeans.

Favorable genotypes associated with at least trait of interest may beidentified by one or more methodologies. In some examples one or moremarkers are used, including but not limited to AFLPs, RFLPs, ASH, SSRs,SNPs, indels, padlock probes, molecular inversion probes, microarrays,sequencing, and the like. In some methods, a target nucleic acid isamplified prior to hybridization with a probe. In other cases, thetarget nucleic acid is not amplified prior to hybridization, such asmethods using molecular inversion probes (see, for example Hardenbol etal. (2003) Nat Biotech 21:673-678). In some examples, the genotyperelated to a specific trait is monitored, while in other examples, agenome-wide evaluation including but not limited to one or more ofmarker panels, library screens, association studies, microarrays, genechips, expression studies, or sequencing such as whole-genomeresequencing and genotyping-by-sequencing (GBS) may be used. In someexamples, no target-specific probe is needed, for example by usingsequencing technologies, including but not limited to next-generationsequencing methods (see, for example, Metzker (2010) Nat Rev Genet11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such assequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina GenomeAnalyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation(e.g., SOLiD from Applied Biosystems, and Polnator system from AzcoBiotech), and single molecule sequencing (SMS or third-generationsequencing) which eliminate template amplification (e.g., Helicossystem, and PacBio RS system from Pacific BioSciences). Furthertechnologies include optical sequencing systems (e.g., Starlight fromLife Technologies), and nanopore sequencing (e.g., GridION from OxfordNanopore Technologies). Each of these may be coupled with one or moreenrichment strategies for organellar or nuclear genomes in order toreduce the complexity of the genome under investigation via PCR,hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoSONE 6:e19379), and expression methods. In some examples, no referencegenome sequence is needed in order to complete the analysis.

The use of marker assisted selection (MAS) to select a soybean plant orgermplasm which has a certain marker locus, haplotype or marker profileis provided. For instance, in certain examples a soybean plant orgermplasm possessing a certain predetermined favorable marker locus orhaplotype will be selected via MAS. In certain other examples, a soybeanplant or germplasm possessing a certain predetermined favorable markerprofile will be selected via MAS.

Using MAS, soybean plants or germplasm can be selected for markers ormarker alleles that positively correlate with soybean cyst nematoderesistance, without actually raising soybean and measuring forresistance (or, contrawise, soybean plants can be selected against ifthey possess markers that negatively correlate with resistance). MAS isa powerful tool to select for desired phenotypes and for introgressingdesired traits into cultivars of soybean (e.g., introgressing desiredtraits into elite lines). MAS is easily adapted to high throughputmolecular analysis methods that can quickly screen large numbers ofplant or germplasm genetic material for the markers of interest and ismuch more cost effective than raising and observing plants for visibletraits.

In some embodiments, the molecular markers or marker loci are detectedusing a suitable amplification-based detection method. In these types ofmethods, nucleic acid primers are typically hybridized to the conservedregions flanking the polymorphic marker region. In certain methods,nucleic acid probes that bind to the amplified region are also employed.In general, synthetic methods for making oligonucleotides, includingprimers and probes, are well known in the art. For example,oligonucleotides can be synthesized chemically according to the solidphase phosphoramidite triester method described by Beaucage andCaruthers (1981) Tetrahedron Letts 22:1859-1862, e.g., using acommercially available automated synthesizer, e.g., as described inNeedham-VanDevanter, et al. (1984) Nucleic Acids Res. 12:6159-6168.Oligonucleotides, including modified oligonucleotides, can also beordered from a variety of commercial sources known to persons of skillin the art.

It will be appreciated that suitable primers and probes to be used canbe designed using any suitable method. It is not intended that theinvention be limited to any particular primer, primer pair or probe. Forexample, primers can be designed using any suitable software program,such as LASERGENE® or Primer3.

It is not intended that the primers be limited to generating an ampliconof any particular size. For example, the primers used to amplify themarker loci and alleles herein are not limited to amplifying the entireregion of the relevant locus. In some embodiments, marker amplificationproduces an amplicon at least 20 nucleotides in length, oralternatively, at least 50 nucleotides in length, or alternatively, atleast 100 nucleotides in length, or alternatively, at least 200nucleotides in length.

Non-limiting examples of polynucleotide primers useful for detecting themarker loci provided herein are provided in Table 2 and 3 and include,for example, SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186,187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200,201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214,215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228,229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242,243, 244, 245, 246, 247, and/or 248 or variants or fragments thereof.

PCR, RT-PCR, and LCR are in particularly broad use as amplification andamplification-detection methods for amplifying nucleic acids of interest(e.g., those comprising marker loci), facilitating detection of themarkers. Details regarding the use of these and other amplificationmethods are well known in the art and can be found in any of a varietyof standard texts. Details for these techniques can also be found innumerous journal and patent references, such as Mullis, et al. (1987)U.S. Pat. No. 4,683,202; Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47;Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173; Guatelli, etal., (1990) Proc. Natl. Acad. Sci. USA87:1874; Lomell, et al., (1989) J.Clin. Chem. 35:1826; Landegren, et al., (1988) Science 241:1077-1080;Van Brunt, (1990) Biotechnology 8:291-294; Wu and Wallace, (1989) Gene4:560; Barringer, et al., (1990) Gene 89:117, and Sooknanan and Malek,(1995) Biotechnology 13:563-564.

Such nucleic acid amplification techniques can be applied to amplifyand/or detect nucleic acids of interest, such as nucleic acidscomprising marker loci. Amplification primers for amplifying usefulmarker loci and suitable probes to detect useful marker loci or togenotype SNP alleles are provided. For example, exemplary primers andprobes are provided in SEQ ID NOS: 1-110 and in Tables 2 and 4, and thegenomic loci comprising the various marker loci provided herein areprovided in SEQ ID NOS: 135-158 and in Table 6. Non-limiting examples ofamplicon sequences comprising the marker loci provided herein areprovided in Table 8. In other embodiments, exemplary primers and probesare provided in SEQ ID NOS: 159-248 and in Tables 3 and 5, and thegenomic loci comprising the various marker loci provided herein areprovided in SEQ ID NOS: 339-337 and in Table 7. However, one of skillwill immediately recognize that other primer and probe sequences couldalso be used. For instance primers to either side of the given primerscan be used in place of the given primers, so long as the primers canamplify a region that includes the allele to be detected, as can primersand probes directed to other SNP marker loci. Further, it will beappreciated that the precise probe to be used for detection can vary,e.g., any probe that can identify the region of a marker amplicon to bedetected can be substituted for those examples provided herein. Further,the configuration of the amplification primers and detection probes can,of course, vary. Thus, the compositions and methods are not limited tothe primers and probes specifically recited herein.

In certain examples, probes will possess a detectable label. Anysuitable label can be used with a probe. Detectable labels suitable foruse with nucleic acid probes include, for example, any compositiondetectable by spectroscopic, radioisotopic, photochemical, biochemical,immunochemical, electrical, optical, or chemical means. Useful labelsinclude biotin for staining with labeled streptavidin conjugate,magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetriclabels. Other labels include ligands, which bind to antibodies labeledwith fluorophores, chemiluminescent agents, and enzymes. A probe canalso constitute radiolabelled PCR primers that are used to generate aradiolabelled amplicon. Labeling strategies for labeling nucleic acidsand corresponding detection strategies can be found, e.g., in Haugland(1996) Handbook of Fluorescent Probes and Research Chemicals SixthEdition by Molecular Probes, Inc. (Eugene Oreg.); or Haugland (2001)Handbook of Fluorescent Probes and Research Chemicals Eighth Edition byMolecular Probes, Inc. (Eugene Oreg.).

Detectable labels may also include reporter-quencher pairs, such as areemployed in Molecular Beacon and TaqMan™ probes. The reporter may be afluorescent organic dye modified with a suitable linking group forattachment to the oligonucleotide, such as to the terminal 3′ carbon orterminal 5′ carbon. The quencher may also be an organic dye, which mayor may not be fluorescent, depending on the embodiment. Generally,whether the quencher is fluorescent or simply releases the transferredenergy from the reporter by non-radiative decay, the absorption band ofthe quencher should at least substantially overlap the fluorescentemission band of the reporter to optimize the quenching. Non-fluorescentquenchers or dark quenchers typically function by absorbing energy fromexcited reporters, but do not release the energy radiatively.

Selection of appropriate reporter-quencher pairs for particular probesmay be undertaken in accordance with known techniques. Fluorescent anddark quenchers and their relevant optical properties from whichexemplary reporter-quencher pairs may be selected are listed anddescribed, for example, in Berlman, Handbook of Fluorescence Spectra ofAromatic Molecules, 2nd ed., Academic Press, New York, 1971, the contentof which is incorporated herein by reference. Examples of modifyingreporters and quenchers for covalent attachment via common reactivegroups that can be added to an oligonucleotide in the present inventionmay be found, for example, in Haugland, Handbook of Fluorescent Probesand Research Chemicals, Molecular Probes of Eugene, Oreg., 1992, thecontent of which is incorporated herein by reference.

In certain examples, reporter-quencher pairs are selected from xanthenedyes including fluoresceins and rhodamine dyes. Many suitable forms ofthese compounds are available commercially with substituents on thephenyl groups, which can be used as the site for bonding or as thebonding functionality for attachment to an oligonucleotide. Anotheruseful group of fluorescent compounds for use as reporters are thenaphthylamines, having an amino group in the alpha or beta position.Included among such naphthylamino compounds are1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonateand 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include3-phenyl-7-isocyanatocoumarin; acridines such as9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide;benzoxadiazoles; stilbenes; pyrenes and the like. In certain otherexamples, the reporters and quenchers are selected from fluorescein andrhodamine dyes. These dyes and appropriate linking methodologies forattachment to oligonucleotides are well known in the art.

Suitable examples of reporters may be selected from dyes such as SYBRgreen, 5-carboxyfluorescein (5-FAM™ available from Applied Biosystems ofFoster City, Calif.), 6-carboxyfluorescein (6-FAM),tetrachloro-6-carboxyfluorescein (TET),2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein,hexachloro-6-carboxyfluorescein (HEX),6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TET™ available fromApplied Biosystems), carboxy-X-rhodamine (ROX),6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOE™ availablefrom Applied Biosystems), VIC™ dye products available from MolecularProbes, Inc., NED™ dye products available from Applied Biosystems, andthe like. Suitable examples of quenchers may be selected from6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo) benzoicacid (DABYL), tetramethylrhodamine (TAMRA), BHQ-0™, BHQ-1™, BHQ-2™, andBHQ-3™, each of which are available from Biosearch Technologies, Inc. ofNovato, Calif., QSY-7™, QSY-9™, QSY-21™ and QSY-35™, each of which areavailable from Molecular Probes, Inc., and the like.

In one aspect, real time PCR or LCR is performed on the amplificationmixtures described herein, e.g., using molecular beacons or TaqMan™probes. A molecular beacon (MB) is an oligonucleotide which, underappropriate hybridization conditions, self-hybridizes to form a stem andloop structure. The MB has a label and a quencher at the termini of theoligonucleotide; thus, under conditions that permit intra-molecularhybridization, the label is typically quenched (or at least altered inits fluorescence) by the quencher. Under conditions where the MB doesnot display intra-molecular hybridization (e.g., when bound to a targetnucleic acid, such as to a region of an amplicon during amplification),the MB label is unquenched. Details regarding standard methods of makingand using MBs are well established in the literature and MBs areavailable from a number of commercial reagent sources. See also, e.g.,Leone, et al., (1995) Molecular beacon probes combined withamplification by NASBA enable homogenous real-time detection of RNA,Nucleic Acids Res. 26:2150-2155; Tyagi and Kramer, (1996) Molecularbeacons: probes that fluoresce upon hybridization, Nature Biotechnology14:303-308; Blok and Kramer, (1997) Amplifiable hybridization probescontaining a molecular switch, Mol Cell Probes 11:187-194; Hsuih. etal., (1997) Novel, ligation-dependent PCR assay for detection ofhepatitis C in serum, J Clin Microbiol 34:501-507; Kostrikis, et al.,(1998) Molecular beacons: spectral genotyping of human alleles, Science279:1228-1229; Sokol, et al., (1998) Real time detection of DNA:RNAhybridization in living cells, Proc. Natl. Acad. Sci. U.S.A.95:11538-11543; Tyagi, et al., (1998) Multicolor molecular beacons forallele discrimination, Nature Biotechnology 16:49-53; Bonnet, et al.,(1999) Thermodynamic basis of the chemical specificity of structured DNAprobes, Proc. Natl. Acad. Sci. U.S.A. 96:6171-6176; Fang, et al. (1999)Designing a novel molecular beacon for surface-immobilized DNAhybridization studies, J. Am. Chem. Soc. 121:2921-2922; Marras, et al.,(1999) Multiplex detection of single-nucleotide variation usingmolecular beacons, Genet. Anal. Biomol. Eng. 14:151-156; and Vet, etal., (1999) Multiplex detection of four pathogenic retroviruses usingmolecular beacons, Proc. Natl. Acad. Sci. U.S.A. 96:6394-6399.Additional details regarding MB construction and use is found in thepatent literature, e.g., U.S. Pat. Nos. 5,925,517; 6,150,097; and6,037,130.

Another real-time detection method is the 5′-exonuclease detectionmethod, also called the TaqMan™ assay, as set forth in U.S. Pat. Nos.5,804,375; 5,538,848; 5,487,972; and 5,210,015, each of which is herebyincorporated by reference in its entirety. In the TaqMan™ assay, amodified probe, typically 10-25 nucleic acids in length, is employedduring PCR which binds intermediate to or between the two members of theamplification primer pair. The modified probe possesses a reporter and aquencher and is designed to generate a detectable signal to indicatethat it has hybridized with the target nucleic acid sequence during PCR.As long as both the reporter and the quencher are on the probe, thequencher stops the reporter from emitting a detectable signal. However,as the polymerase extends the primer during amplification, the intrinsic5′ to 3′ nuclease activity of the polymerase degrades the probe,separating the reporter from the quencher, and enabling the detectablesignal to be emitted. Generally, the amount of detectable signalgenerated during the amplification cycle is proportional to the amountof product generated in each cycle.

It is well known that the efficiency of quenching is a strong functionof the proximity of the reporter and the quencher, i.e., as the twomolecules get closer, the quenching efficiency increases. As quenchingis strongly dependent on the physical proximity of the reporter andquencher, the reporter and the quencher are preferably attached to theprobe within a few nucleotides of one another, usually within 30nucleotides of one another, more preferably with a separation of fromabout 6 to 16 nucleotides. Typically, this separation is achieved byattaching one member of a reporter-quencher pair to the 5′ end of theprobe and the other member to a nucleotide about 6 to 16 nucleotidesaway, in some cases at the 3′ end of the probe.

Separate detection probes can also be omitted in amplification/detectionmethods, e.g., by performing a real time amplification reaction thatdetects product formation by modification of the relevant amplificationprimer upon incorporation into a product, incorporation of labelednucleotides into an amplicon, or by monitoring changes in molecularrotation properties of amplicons as compared to unamplified precursors(e.g., by fluorescence polarization).

Further, it will be appreciated that amplification is not a requirementfor marker detection—for example, one can directly detect unamplifiedgenomic DNA simply by performing a Southern blot on a sample of genomicDNA. Procedures for performing Southern blotting, amplification e.g.,(PCR, LCR, or the like), and many other nucleic acid detection methodsare well established and are taught, e.g., in Sambrook, et al.,Molecular Cloning—A Laboratory Manual (3d ed.), Vol. 1-3, Cold SpringHarbor Laboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); CurrentProtocols in Molecular Biology, F. M. Ausubel, et al., eds., CurrentProtocols, a joint venture between Greene Publishing Associates, Inc.and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”))and PCR Protocols A Guide to Methods and Applications (Innis, et al.,eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Additionaldetails regarding detection of nucleic acids in plants can also befound, e.g., in Plant Molecular Biology (1993) Croy (ed.) BIOSScientific Publishers, Inc.

Other techniques for detecting SNPs can also be employed, such as allelespecific hybridization (ASH). ASH technology is based on the stableannealing of a short, single-stranded, oligonucleotide probe to acompletely complementary single-stranded target nucleic acid. Detectionis via an isotopic or non-isotopic label attached to the probe. For eachpolymorphism, two or more different ASH probes are designed to haveidentical DNA sequences except at the polymorphic nucleotides. Eachprobe will have exact homology with one allele sequence so that therange of probes can distinguish all the known alternative allelesequences. Each probe is hybridized to the target DNA. With appropriateprobe design and hybridization conditions, a single-base mismatchbetween the probe and target DNA will prevent hybridization.

Real-time amplification assays, including MB or TaqMan™ based assays,are especially useful for detecting SNP alleles. In such cases, probesare typically designed to bind to the amplicon region that includes theSNP locus, with one allele-specific probe being designed for eachpossible SNP allele. For instance, if there are two known SNP allelesfor a particular SNP locus, “A” or “C,” then one probe is designed withan “A” at the SNP position, while a separate probe is designed with a“C” at the SNP position. While the probes are typically identical to oneanother other than at the SNP position, they need not be. For instance,the two allele-specific probes could be shifted upstream or downstreamrelative to one another by one or more bases. However, if the probes arenot otherwise identical, they should be designed such that they bindwith approximately equal efficiencies, which can be accomplished bydesigning under a strict set of parameters that restrict the chemicalproperties of the probes. Further, a different detectable label, forinstance a different reporter-quencher pair, is typically employed oneach different allele-specific probe to permit differential detection ofeach probe. In certain examples, each allele-specific probe for acertain SNP locus is 11-20 nucleotides in length, dual-labeled with aflorescence quencher at the 3′ end and either the 6-FAM(6-carboxyfluorescein) or VIC(4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) fluorophore at the 5′end.

To effectuate SNP allele detection, a real-time PCR reaction can beperformed using primers that amplify the region including the SNP locus,for instance the sequences listed in Table 4, the reaction beingperformed in the presence of all allele-specific probes for the givenSNP locus. By then detecting signal for each detectable label employedand determining which detectable label(s) demonstrated an increasedsignal, a determination can be made of which allele-specific probe(s)bound to the amplicon and, thus, which SNP allele(s) the ampliconpossessed. For instance, when 6-FAM- and VIC-labeled probes areemployed, the distinct emission wavelengths of 6-FAM (518 nm) and VIC(554 nm) can be captured. A sample that is homozygous for one allelewill have fluorescence from only the respective 6-FAM or VICfluorophore, while a sample that is heterozygous at the analyzed locuswill have both 6-FAM and VIC fluorescence.

The KASPar® and Illumina® Detection Systems are additional examples ofcommercially-available marker detection systems. KASPar® is ahomogeneous fluorescent genotyping system which utilizes allele specifichybridization and a unique form of allele specific PCR (primerextension) in order to identify genetic markers (e.g. a particular SNPlocus associated with soybean cyst nematode resistance). Illumina®detection systems utilize similar technology in a fixed platform format.The fixed platform utilizes a physical plate that can be created with upto 384 markers. The Illumina® system is created with a single set ofmarkers that cannot be changed and utilizes dyes to indicate markerdetection.

These systems and methods represent a wide variety of availabledetection methods which can be utilized to detect markers associatedwith improved resistance to soybean cyst nematode, but any othersuitable method could also be used.

Introgression of soybean cyst nematode resistance into non-tolerant orless-tolerant soybean germplasm is provided. Any method forintrogressing one or more marker loci into soybean plants known to oneof skill in the art can be used. Typically, a first soybean germplasmthat contains soybean cyst nematode resistance derived from a particularmarker locus, haplotype or marker profile and a second soybean germplasmthat lacks such resistance derived from the marker locus, haplotype ormarker profile are provided. The first soybean germplasm may be crossedwith the second soybean germplasm to provide progeny soybean germplasm.These progeny germplasm are screened to determine the presence ofsoybean cyst nematode resistance derived from the marker locus,haplotype or marker profile, and progeny that tests positive for thepresence of resistance derived from the marker locus, haplotype ormarker profile are selected as being soybean germplasm into which themarker locus, haplotype or marker profile has been introgressed. Methodsfor performing such screening are well known in the art and any suitablemethod can be used.

One application of MAS is to use the resistance markers, haplotypes ormarker profiles to increase the efficiency of an introgression orbackcrossing effort aimed at introducing a resistance trait into adesired (typically high yielding) background. In marker assistedbackcrossing of specific markers from a donor source, e.g., to an elitegenetic background, one selects among backcross progeny for the donortrait and then uses repeated backcrossing to the elite line toreconstitute as much of the elite background's genome as possible.

Thus, the markers and methods can be utilized to guide marker assistedselection or breeding of soybean varieties with the desired complement(set) of allelic forms of chromosome segments associated with superioragronomic performance (resistance, along with any other availablemarkers for yield, disease resistance, etc.). Any of the disclosedmarker loci, marker alleles, haplotypes, or marker profiles can beintroduced into a soybean line via introgression, by traditionalbreeding (or introduced via transformation, or both) to yield a soybeanplant with superior agronomic performance. The number of allelesassociated with resistance that can be introduced or be present in asoybean plant ranges from 1 to the number of alleles disclosed herein,each integer of which is incorporated herein as if explicitly recited.

The markers and methods provided herein can also be utilized to guidemarker assisted selection or breeding of soybean varieties comprisingother soybean cyst nematode resistance markers or alleles to create amolecular stack for soybean cyst nematode resistance. For example, anyof the marker loci provided herein can be introduced into a soybean linehaving one or more of the soybean cyst nematode resistance alleles rhg1,rhg2, rhg3, rhg4 or rhg5. In one embodiment, any one or more of themarker loci provided herein can be stacked with the rhg1 allele. Inanother embodiment, any one or more of the marker loci provided hereincan be stacked with the rhg4 allele. In a further embodiment, any one ormore of the marker loci provided herein can be stacked with the rhg1 andrhg4 alleles. For example, any of the marker loci provided herein can beintroduced into a soybean line having one or more of the soybean cystnematode resistance loci rhg1, rhg2, rhg3 or rhg5. In one embodiment,any one or more of the marker loci provided herein can be stacked withthe rhg1 locus. In another embodiment, any one or more of the markerloci provided herein can be stacked with the rhg2 locus. In a furtherembodiment, any one or more of the marker loci provided herein can bestacked with the rhg1 and rhg2 loci.

This also provides a method of making a progeny soybean plant and theseprogeny soybean plants, per se. The method comprises crossing a firstparent soybean plant with a second soybean plant and growing the femalesoybean plant under plant growth conditions to yield soybean plantprogeny. Methods of crossing and growing soybean plants are well withinthe ability of those of ordinary skill in the art. Such soybean plantprogeny can be assayed for alleles associated with resistance and,thereby, the desired progeny selected. Such progeny plants or seed canbe sold commercially for soybean production, used for food, processed toobtain a desired constituent of the soybean, or further utilized insubsequent rounds of breeding. At least one of the first or secondsoybean plants is a soybean plant in that it comprises at least one ofthe marker loci or marker profiles, such that the progeny are capable ofinheriting the marker locus or marker profile.

Often, a method is applied to at least one related soybean plant such asfrom progenitor or descendant lines in the subject soybean plantspedigree such that inheritance of the desired resistance can be traced.The number of generations separating the soybean plants being subject tothe methods provided herein will generally be from 1 to 20, commonly 1to 5, and typically 1, 2, or 3 generations of separation, and quiteoften a direct descendant or parent of the soybean plant will be subjectto the method (i.e., 1 generation of separation).

Genetic diversity is important for long term genetic gain in anybreeding program. With limited diversity, genetic gain will eventuallyplateau when all of the favorable alleles have been fixed within theelite population. One objective is to incorporate diversity into anelite pool without losing the genetic gain that has already been madeand with the minimum possible investment. MAS provides an indication ofwhich genomic regions and which favorable alleles from the originalancestors have been selected for and conserved over time, facilitatingefforts to incorporate favorable variation from exotic germplasm sources(parents that are unrelated to the elite gene pool) in the hopes offinding favorable alleles that do not currently exist in the elite genepool.

For example, the markers, haplotypes, primers, probes, and markerprofiles can be used for MAS in crosses involving elite x exotic soybeanlines by subjecting the segregating progeny to MAS to maintain majoryield alleles, along with the resistance marker alleles herein.

As an alternative to standard breeding methods of introducing traits ofinterest into soybean (e.g., introgression), transgenic approaches canalso be used to create transgenic plants with the desired traits. Inthese methods, exogenous nucleic acids that encode a desired markerloci, marker profile or haplotype are introduced into target plants orgermplasm. For example, a nucleic acid that codes for a resistance traitis cloned, e.g., via positional cloning, and introduced into a targetplant or germplasm.

Experienced plant breeders can recognize tolerant soybean plants in thefield, and can select the tolerant individuals or populations forbreeding purposes or for propagation. In this context, the plant breederrecognizes “resistant” and “non-resistant” or “susceptible” soybeanplants. However, plant resistance is a phenotypic spectrum consisting ofextremes in resistance and susceptibility, as well as a continuum ofintermediate resistance phenotypes. Evaluation of these intermediatephenotypes using reproducible assays are of value to scientists who seekto identify genetic loci that impart resistance, to conduct markerassisted selection for tolerant populations, and to use introgressiontechniques to breed a resistance trait into an elite soybean line, forexample.

By “improved resistance” is intended that the plants show a decrease inthe disease symptoms that are the outcome of plant exposure to soybeancyst nematode. That is, the damage caused by soybean cyst nematode isprevented, or alternatively, the disease symptoms caused by soybean cystnematode is minimized or lessened. Thus, improved resistance to soybeancyst nematode can result in reduction of the disease symptoms by atleast about 2% to at least about 6%, at least about 5% to about 50%, atleast about 10% to about 60%, at least about 30% to about 70%, at leastabout 40% to about 80%, or at least about 50% to about 90% or greater.Hence, the methods provided herein can be utilized to protect plantsfrom soybean cyst nematode.

Screening and selection of soybean cyst nematode tolerant soybean plantsmay be performed, for example, by exposing plants to soybean cystnematode and selecting those plants showing resistance to soybean cystnematode. Various assays can be used to measure resistance or improvedresistance to soybean cyst nematode. For example, soybean cyst nematoderesistance can be determined by visual observations after plant exposureto a particular race of soybean cyst nematode, such as race 1, 2, 3, 5or 14. Scores range from 1 to 9 and indicate visual observations ofresistance as compared to other genotypes in the test. A score of 1indicates soybean cyst nematode are able to infect the plant and causeyield loss, while a score of 9 indicates soybean cyst nematoderesistance. Preliminary scores are reported as double digits, forexample, ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

Non-limiting examples of soybean cyst nematode resistance phenotypicscreening are described in detail below.

Multiple populations of Heterodera glycines are maintained and increasedon host plants. These populations are used to identify, purify, andcharacterize elite soybean varieties for resistance to soybean cystnematode. The following races of soybean cyst nematode are maintained:Race 1 (Type HG 2.5), Race 2 (Type HG 1.2.5.7), Race 3 (Type HG 0 orType HG 7), Race 5 (Type HG 2.5.7), and Race 14 (Type HG 1.3.6.7).

Eggs or second stage juveniles (J2) are used to inoculate host plants toincrease their population. Soybean cyst nematode infestation requires aminimum 35 days before the cysts reach maturity and can be used toinoculate soybean experiments. Cyst eggs/J2 inoculant is harvestedthrough a series of washings, grindings, and screenings. Screens areused progressing from larger to smaller sizes, ending with a #500 (25μm) screen.

Soybean plants are grown in cones. Cones are long containersapproximately 12 inches long and 1.5 inches in diameter at the top(e.g., Ray Leach Cone-tainers™). The cone is designed to easily removethe root mass. Three to seven days after planting, an inoculum channelis made in the cone containing the experimental line by poking a 4 inchhole with a 10 ml pipette tip. One ml of inoculum is dispensed into thechannel. The plants are watered manually for the duration of the test,with watering being moderately light during the first 3-5 days until J2infects the roots.

Plants are scored approximately 28-35 days following inoculation whencyst reproduction on susceptible checks is sufficiently high. Plants areremoved from their cones and the soil is removed from the roots bygently dipping the roots into a bucket of water. The plants are screenedto identify native resistance to one or more of the five races ofsoybean cyst nematode inoculated using a combination of three methods(1) visual 9-6-1 score; (2) visual full count; and/or (3) microscopecount score depending on the stage of the line when screened. Ingeneral, lines earlier in the development cycle (R1-R2) are screened bythe visual 9-6-1 method, and lines that have progressed to laterdevelopment phases (R3-R5) are screened by the visual full count and/ormicroscope count method(s).

One typical phenotyping method is a visual evaluation of the roots.Susceptible checks are first evaluated for the development of cysts onthe root system. These counts are recorded and averaged across theexperiment to determine the susceptible (SUS) check average. Roots fromthe test plants are then scored based on a comparison with the averageof the susceptible checks as follows:

9=0-15% of the susceptible checks average

6=16-40% of the susceptible checks average

1=≧41% of the susceptible checks average

Visual Counts:

In this method, known checks are counted and reported in full. Observedcysts on the test plants are counted for comparison to the susceptiblecheck plant scores. Cyst counts are converted to 1-9 scores based on thefemale index (FI). The female index (FI) is the percentage of the numberof females cysts produced on each experimental line divided by thenumber produced on a standard susceptible soybean check, then the resultis multiplied by 100. A low FI (<10) means that the soybean cystnematode population is not able to reproduce well on the test line, ahigh FI means that the soybean cyst nematode population is able toreproduce well on the test line.

Microscope Counts:

Cysts counts for soybean cyst nematode assays for checks andexperimental line are determined by washing cysts from roots andcounting the number of cysts under the microscope.

At about 28-35 days after inoculation, roots from the susceptible checkcontrols are examined for yellow cysts to assess whether to begin theprocess of evaluating the test. Experimental lines are compared withknown standard checks. Once adequate levels of cysts are detected on thecheck varieties, plants from the test lines are removed from cones oneat a time. Soil is removed from roots by gently dipping the roots into abucket of water. The root tissue is placed on a 850 micron (#20) poresieve stacked over a 250 micron (#60) pore sieve and sprayed with a jetof water to dislodge cysts from the roots. Collected cysts are rinsedfrom the #60 sieve into a clean labeled cup using no more than 30 mls ofadditional water.

Once all the samples are collected, each sample is counted using agridded counting dish under a stereo microscope. The number of cystscounted are recorded for each sample. Cyst counts on the test plants areconverted to the 1-9 scoring scale based on the female index (FI)described above.

The following exemplary soybean cyst nematode checks, as depicted inTable 6, can be planted and used to monitor cyst development:

TABLE 10 Exemplary soybean cyst nematode checks. Race 1 Race 2 Race 3Race 5 Race 14 92B12 RES 95M60 RES 9182 RES 92B12 RES 9182 RES 9281 SUS9281 SUS 9281 SUS 9281 SUS 9281 SUS 9234 RES PI437654 RES 9234 RES 9234RES 9234 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS 91M12 MR 9234MR 93B15 MR 91M12 SUS 93B15 MR RES = Resistant; SUS = Susceptible; and,MR = Moderately Resistant

In some examples, a kit or an automated system for detecting markerloci, haplotypes, and marker profiles, and/or correlating the markerloci, haplotypes, and marker profiles with a desired phenotype (e.g.,soybean cyst nematode resistance) are provided. As used herein, “kit”refers to a set of reagents for the purpose of performing the variousmethods of detecting or identifying herein, more particularly, theidentification and/or the detection of a soybean plant or germplasmhaving improved resistance to soybean cyst nematode.

In one embodiment, a kit for detecting or selecting at least one soybeanplant or soybean germplasm with improved resistance to soybean cystnematode is provided. Such a kit comprises (a) primers or probes fordetecting one or more marker loci associated with resistance to soybeancyst nematode, wherein at least one of the primers and probes in the kitare capable of detecting a marker locus, wherein the marker locus is:(i) between about marker Sat_123 and about marker Satt453 on linkagegroup B1; (ii) between about marker Sat_207 and about marker Satt713 onlinkage group C1; or (iii) between about marker Satt574 and about markerSatt615 on linkage group D2; and (b) instructions for using the primersor probes for detecting the one or more marker loci and correlating thedetected marker loci with predicted resistance to soybean cyst nematode.

In a specific embodiment, the primers and probes of the kit are capableof detecting a marker locus comprising: (a) S04196-1-B, S04938-1-A,S04937-1-Q1, S08344-1-Q1, S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1,S06803-1, S04197-1 on linkage group B1, or a closely linked marker; (b)S07162-1-Q1 on linkage group C1, or a closely linked marker; or (c)S07161-1-Q1 on linkage group D2, or a closely linked marker.

In one embodiment, a kit for detecting or selecting at least one soybeanplant or soybean germplasm with improved resistance to soybean cystnematode is provided. Such a kit comprises (I) primers or probes fordetecting one or more marker loci associated with resistance to soybeancyst nematode, wherein at least one of the primers and probes in the kitare capable of detecting a marker locus, wherein the marker locus is:(a) is flanked by S04348 and S01999 on linkage group B1; (b) two or moremarker locus within 30 cM of one or more of S04348, S01209, or S01999 onlinkage group B1; (c) is within 10 cM of one or more of S04348, S01209,or S01999 on linkage group B1; (d) comprises S04348-1-A, S01209-1-A,S01999-1-A, or a marker closely linked thereto on linkage group B1; (e)is flanked by S01209 and S01999 on linkage group B1; (f) is selectedfrom the group consisting of S04937-2-A, S04937-1-Q1, S04938-1-A,S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1, S06787-2-Q1,S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1, S06805-1-Q1,S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, or S06792-1-Q1 or amarker closely linked thereto on linkage group B1; (g) is flanked bySatt557 and Satt307 on linkage group C2; (h) is flanked by S03252 andS02112 on linkage group C2; (i) is within 30 cM of one or more of S03252or S02112 on linkage group C2; (j) is within 10 cM of one or more ofS03252 or S02112 on linkage group C2; (k) comprises S03252-1-A,S02112-1-A, or a marker closely linked thereto on linkage group C2; (1)is in an interval comprising the bottom 30 cM of linkage group E, forexample from about 66 cM to the end; (m) is flanked by BARC-062799-18070to the end of linkage group E; (n) is flanked by Sat_107 to the end oflinkage group E; (o) is flanked by S00350 to S02183 on linkage group E;(p) is within 30 cM of one or more of S00350 or S02183 on linkage groupE; (q) is within 10 cM of one or more of S00350 or S02183 on linkagegroup E; (r) comprises S00350-1-A, S02183-1-A, or a marker closelylinked thereto on linkage group E; (s) is in an interval comprising thetop 30 cM of linkage group L, for example from about 0-30 cM; (t) is inan interval is flanked by S02074 and S03991 on linkage group L; (u) iswithin 30 cM of one or more of S02074 or S03991 on linkage group L; (v)is within 10 cM of one or more of S02074 or S03991 on linkage group L;(w) comprises S02074-1-A, S03991-1-A, or a marker closely linked theretoon linkage group L; (x) is flanked by marker locus S00875 and aboutmarker S02621 on linkage group D1b; (y) is flanked by S00479 and S02136on linkage group D1b; (z) is within 30 cM of one or more of S00479,S02136, S00875, S12875, S12950, S12947, S12933, S12853, S03246, S01519,S12962, S00144, S08166, S08177, S01081, and S02621 on linkage group D1b;(aa) is within 10 cM of one or more of S00479, S02136, S00875, S12875,S12950, S12947, S12933, S12853, S03246, S01519, S12962, S00144, S08166,S08177, S01081, and S02621 on linkage group D1b; (ab) comprises one ormore of S01519-1-A, S08177-1-Q1, S00479-1-A, S02136-1-A, S00875-1-A,S12875-1-Q1, S12950-1-Q1, S12947-1-Q1, S12933-1-Q1, S12853-1-Q1,S03246-1-A or S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, andS02621-1-A, or a marker closely linked thereto on linkage group D1b;(ac) is flanked by Sat_264 and about BARC-020449-04623 on linkage groupB2; (ad) is flanked by S02874 and S04785 on linkage group B2; (ae) iswithin 30 cM of one or more of S02864 and S04785 on linkage group B2;(af) is within 10 cM of one or more of S02864 and S04785 on linkagegroup B2; and/or (ag) comprises S02874-1-A, S04785-1-A, or a markerclosely linked thereto on linkage group B2; and (II) instructions forusing the primers or probes for detecting the one or more marker lociand correlating the detected marker loci with predicted resistance tosoybean cyst nematode.

In a specific embodiment, the primers and probes of the kit are capableof detecting a marker locus comprising a marker that: (a) is flanked byS04348 and S01999 on linkage group B1; (b) two or more marker locuswithin 30 cM of one or more of S04348, S01209, or S01999 on linkagegroup B1; (c) is within 10 cM of one or more of S04348, S01209, orS01999 on linkage group B1; (d) comprises S04348-1-A, S01209-1-A,S01999-1-A, or a marker closely linked thereto on linkage group B1; (e)is flanked by S01209 and S01999 on linkage group B1; (f) is selectedfrom the group consisting of S04937-2-A, S04937-1-Q1, S04938-1-A,S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1, S06787-2-Q1,S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1, S06805-1-Q1,S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, or S06792-1-Q1 or amarker closely linked thereto on linkage group B1; (g) is flanked bySatt557 and Satt307 on linkage group C2; (h) is flanked by S03252 andS02112 on linkage group C2; (i) is within 30 cM of one or more of S03252or S02112 on linkage group C2; (j) is within 10 cM of one or more ofS03252 or S02112 on linkage group C2; (k) comprises S03252-1-A,S02112-1-A, or a marker closely linked thereto on linkage group C2; (1)is in an interval comprising the bottom 30 cM of linkage group E, forexample from about 66 cM to the end; (m) is flanked by BARC-062799-18070to the end of linkage group E; (n) is flanked by Sat_107 to the end oflinkage group E; (o) is flanked by S00350 to S02183 on linkage group E;(p) is within 30 cM of one or more of S00350 or S02183 on linkage groupE; (q) is within 10 cM of one or more of S00350 or S02183 on linkagegroup E; (r) comprises S00350-1-A, S02183-1-A, or a marker closelylinked thereto on linkage group E; (s) is in an interval comprising thetop 30 cM of linkage group L, for example from about 0-30 cM; (t) is inan interval is flanked by S02074 and S03991 on linkage group L; (u) iswithin 30 cM of one or more of S02074 or S03991 on linkage group L; (v)is within 10 cM of one or more of S02074 or S03991 on linkage group L;(w) comprises S02074-1-A, S03991-1-A, or a marker closely linked theretoon linkage group L; (x) is flanked by marker locus S00875 and aboutmarker S02621 on linkage group D1b; (y) is flanked by S00479 and S02136on linkage group D1b; (z) is within 30 cM of one or more of S00479,S02136, S00875, S12875, S12950, S12947, S12933, S12853, S03246, S01519,S12962, S00144, S08166, S08177, S01081, and S02621 on linkage group D1b;(aa) is within 10 cM of one or more of S00479, S02136, S00875, S12875,S12950, S12947, S12933, S12853, S03246, S01519, S12962, S00144, S08166,S08177, S01081, and S02621 on linkage group D1b; (ab) comprises one ormore of S01519-1-A, S08177-1-Q1, S00479-1-A, S02136-1-A, S00875-1-A,S12875-1-Q1, S12950-1-Q1, S12947-1-Q1, S12933-1-Q1, S12853-1-Q1,S03246-1-A or S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, andS02621-1-A, or a marker closely linked thereto on linkage group D1b;(ac) is flanked by Sat_264 and about BARC-020449-04623 on linkage groupB2; (ad) is flanked by S02874 and S04785 on linkage group B2; (ae) iswithin 30 cM of one or more of S02864 and S04785 on linkage group B2;(af) is within 10 cM of one or more of S02864 and S04785 on linkagegroup B2; and/or (ag) comprises S02874-1-A, S04785-1-A, or a markerclosely linked thereto on linkage group B2.

Thus, a typical kit or system can include a set of marker probes orprimers configured to detect at least one favorable allele of one ormore marker loci associated with resistance to soybean cyst nematode,for instance a favorable marker locus, haplotype or marker profile.These probes or primers can be configured, for example, to detect themarker loci noted in the tables and examples herein, e.g., using anyavailable allele detection format, such as solid or liquid phase arraybased detection, microfluidic-based sample detection, etc. The systemsand kits can further include packaging materials for packaging theprobes, primers, or instructions, controls such as control amplificationreactions that include probes, primers or template nucleic acids foramplifications, molecular size markers, or the like.

A typical system can also include a detector that is configured todetect one or more signal outputs from the set of marker probes orprimers, or amplicon thereof, thereby identifying the presence orabsence of the allele. A wide variety of signal detection apparatus areavailable, including photo multiplier tubes, spectrophotometers, CCDarrays, scanning detectors, phototubes and photodiodes, microscopestations, galvo-scans, microfluidic nucleic acid amplification detectionappliances and the like. The precise configuration of the detector willdepend, in part, on the type of label used to detect the marker allele,as well as the instrumentation that is most conveniently obtained forthe user. Detectors that detect fluorescence, phosphorescence,radioactivity, pH, charge, absorbance, luminescence, temperature,magnetism or the like can be used. Typical detector examples includelight (e.g., fluorescence) detectors or radioactivity detectors. Forexample, detection of a light emission (e.g., a fluorescence emission)or other probe label is indicative of the presence or absence of amarker allele. Fluorescent detection is generally used for detection ofamplified nucleic acids (however, upstream and/or downstream operationscan also be performed on amplicons, which can involve other detectionmethods). In general, the detector detects one or more label (e.g.,light) emission from a probe label, which is indicative of the presenceor absence of a marker allele. The detector(s) optionally monitors oneor a plurality of signals from an amplification reaction. For example,the detector can monitor optical signals which correspond to “real time”amplification assay results.

System or kit instructions that describe how to use the system or kit orthat correlate the presence or absence of the favorable allele with thepredicted resistance are also provided. For example, the instructionscan include at least one look-up table that includes a correlationbetween the presence or absence of the favorable alleles, haplotypes, ormarker profiles and the predicted resistance. The precise form of theinstructions can vary depending on the components of the system, e.g.,they can be present as system software in one or more integrated unit ofthe system (e.g., a microprocessor, computer or computer readablemedium), or can be present in one or more units (e.g., computers orcomputer readable media) operably coupled to the detector. As noted, inone typical example, the system instructions include at least onelook-up table that includes a correlation between the presence orabsence of the favorable alleles and predicted resistance. Theinstructions also typically include instructions providing a userinterface with the system, e.g., to permit a user to view results of asample analysis and to input parameters into the system.

Isolated polynucleotides comprising the nucleic acid sequences of theprimers and probes provided herein are also encompassed herein. In oneembodiment, the isolated polynucleotide comprises a polynucleotidecapable of detecting a marker locus of the soybean genome comprisingS04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1, S08343-1-Q1,S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1, S07162-1-Q1,S07162-1-Q1, or a marker closely linked thereto.

Isolated polynucleotides comprising the nucleic acid sequences of theprimers and probes provided herein are also encompassed herein. In oneembodiment, the isolated polynucleotide comprises a polynucleotidecapable of detecting a marker locus of the soybean genome comprising amarker locus (a) is flanked by S04348 and S01999 on linkage group B1;(b) two or more marker locus within 30 cM of one or more of S04348,S01209, or S01999 on linkage group B1; (c) is within 10 cM of one ormore of S04348, S01209, or S01999 on linkage group B1; (d) comprisesS04348-1-A, S01209-1-A, S01999-1-A, or a marker closely linked theretoon linkage group B1; (e) is flanked by S01209 and S01999 on linkagegroup B1; (f) is selected from the group consisting of S04937-2-A,S04937-1-Q1, S04938-1-A, S04938-2-A, S06786-2-Q1, S06786-3-Q1,S06786-1-Q1, S06787-2-Q1, S06787-1-Q1, S06803-1-Q1, S06804-1-Q1,S06788-1-Q1, S06805-1-Q1, S06789-1-Q1, S06790-1-Q1, S06791-2-Q1,S06791-1-Q1, or S06792-1-Q1 or a marker closely linked thereto onlinkage group B1; (g) is flanked by Satt557 and Satt307 on linkage groupC2; (h) is flanked by S03252 and S02112 on linkage group C2; (i) iswithin 30 cM of one or more of S03252 or S02112 on linkage group C2; (j)is within 10 cM of one or more of S03252 or S02112 on linkage group C2;(k) comprises S03252-1-A, S02112-1-A, or a marker closely linked theretoon linkage group C2; (1) is in an interval comprising the bottom 30 cMof linkage group E, for example from about 66 cM to the end; (m) isflanked by BARC-062799-18070 to the end of linkage group E; (n) isflanked by Sat_107 to the end of linkage group E; (o) is flanked byS00350 to S02183 on linkage group E; (p) is within 30 cM of one or moreof S00350 or S02183 on linkage group E; (q) is within 10 cM of one ormore of S00350 or S02183 on linkage group E; (r) comprises S00350-1-A,S02183-1-A, or a marker closely linked thereto on linkage group E; (s)is in an interval comprising the top 30 cM of linkage group L, forexample from about 0-30 cM; (t) is in an interval is flanked by S02074and S03991 on linkage group L; (u) is within 30 cM of one or more ofS02074 or S03991 on linkage group L; (v) is within 10 cM of one or moreof S02074 or S03991 on linkage group L; (w) comprises S02074-1-A,S03991-1-A, or a marker closely linked thereto on linkage group L; (x)is flanked by marker locus S00875 and about marker S02621 on linkagegroup D1b; (y) is flanked by S00479 and S02136 on linkage group D1b; (z)is within 30 cM of one or more of S00479, S02136, S00875, S12875,S12950, S12947, S12933, S12853, S03246, S01519, S12962, S00144, S08166,S08177, S01081, and S02621 on linkage group D1b; (aa) is within 10 cM ofone or more of S00479, S02136, S00875, S12875, S12950, S12947, S12933,S12853, S03246, S01519, S12962, S00144, S08166, S08177, S01081, andS02621 on linkage group D1b; (ab) comprises one or more of S01519-1-A,S08177-1-Q1, S00479-1-A, S02136-1-A, S00875-1-A, S12875-1-Q1,S12950-1-Q1, S12947-1-Q1, S12933-1-Q1, S12853-1-Q1, S03246-1-A orS12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, and S02621-1-A, or a markerclosely linked thereto on linkage group D1b; (ac) is flanked by Sat_264and about BARC-020449-04623 on linkage group B2; (ad) is flanked byS02874 and S04785 on linkage group B2; (ae) is within 30 cM of one ormore of S02864 and S04785 on linkage group B2; (af) is within 10 cM ofone or more of S02864 and S04785 on linkage group B2; and/or (ag)comprises S02874-1-A, S04785-1-A, or a marker closely linked thereto onlinkage group B2.

In specific embodiments, the isolated polynucleotide comprises: (a) apolynucleotide comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,84, 85, 86, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170,171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184,185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198,199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212,213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226,227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240,241, 242, 243, 244, 245, 246, 247, and/or 248; (b) a polynucleotidecomprising SEQ ID NOs: 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 249, 250,251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264,265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278,279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292,293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306,307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320,321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334,335, 336, 337, and/or 338; (c) a polynucleotide having at least 90%sequence identity to SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101,102, 103, 104, 105, 106, 107, 108, 109, 110, 159, 160, 161, 162, 163,164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177,178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205,206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219,220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233,234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261,262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275,276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289,290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303,304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317,318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,332, 333, 334, 335, 336, 337, and/or 338; or (d) a polynucleotidecomprising at least 10 contiguous nucleotides of SEQ ID NOs: 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186,187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200,201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214,215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228,229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242,243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256,257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270,271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284,285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298,299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312,313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326,327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, and/or 338.

In certain embodiments, the isolated nucleic acids are capable ofhybridizing under stringent conditions to nucleic acids of a soybeancultivar tolerant to soybean cyst nematode, for instance to particularSNPs that comprise a marker locus, haplotype or marker profile.

As used herein, a substantially identical or complementary sequence is apolynucleotide that will specifically hybridize to the complement of thenucleic acid molecule to which it is being compared under highstringency conditions. A polynucleotide is said to be the “complement”of another polynucleotide if they exhibit complementarity. As usedherein, molecules are said to exhibit “complete complementarity” whenevery nucleotide of one of the polynucleotide molecules is complementaryto a nucleotide of the other. Two molecules are said to be “minimallycomplementary” if they can hybridize to one another with sufficientstability to permit them to remain annealed to one another under atleast conventional “low-stringency” conditions. Similarly, the moleculesare said to be “complementary” if they can hybridize to one another withsufficient stability to permit them to remain annealed to one anotherunder conventional “high-stringency” conditions.

Appropriate stringency conditions which promote DNA hybridization, forexample, 6× sodium chloride/sodium citrate (SSC) at about 45° C.,followed by a wash of 2×SSC at 50° C., are known to those skilled in theart or can be found in Current Protocols in Molecular Biology, JohnWiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Typically, stringent conditionsfor hybridization and detection will be those in which the saltconcentration is less than about 1.5 M Na ion, typically about 0.01 to1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides) and at least about 60° C. for long probes (e.g., greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. Exemplary lowstringency conditions include hybridization with a buffer solution of 30to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C.,and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at50 to 55° C. Exemplary moderate stringency conditions includehybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., anda wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringencyconditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffersmay comprise about 0.1% to about 1% SDS. Duration of hybridization isgenerally less than about 24 hours, usually about 4 to about 12 hours.The duration of the wash time will be at least a length of timesufficient to reach equilibrium.

Non-limiting examples of methods and compositions disclosed herein areas follows:

1. A method of identifying a first soybean plant or a first soybeangermplasm that displays improved resistance to soybean cyst nematode,the method comprising detecting in the genome of said first soybeanplant or in the genome of said first soybean germplasm at least onemarker locus that is associated with the resistance, wherein:

(a) the at least one marker locus is between about marker Sat_123 andabout marker Satt453 on linkage group B1;

(b) the at least one marker locus is between about marker Sat_207 andabout marker Satt713 on linkage group C1; or

(c) the at least one marker locus is between about marker Satt574 andabout marker Satt615 on linkage group D2.

2. The method of embodiment 1, wherein the at least one marker locus ofpart (a) comprises S04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1,S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1 or amarker closely linked thereto.3. The method of embodiment 1, wherein the at least one marker locus ofpart (b) comprises S07162-1-Q1 or a marker closely linked thereto.4. The method of embodiment 1, wherein the at least one marker locus ofpart (c) comprises S07161-1-Q1 or a marker closely linked thereto.5. The method of any one of embodiments 1-4, wherein at least two markerloci are detected.6. The method of embodiment 5, wherein the at least two marker locicomprise a haplotype that is associated with said resistance.7. The method of embodiment 5, wherein the at least two marker locicomprise a marker profile that is associated with said resistance.8. The method of any one of embodiments 1-7, wherein the germplasm is asoybean variety.9. The method of any one of embodiments 1-8, wherein the method furthercomprises selecting the first soybean plant or first soybean germplasmor a progeny thereof having the at least one marker locus.10. The method of embodiment 9, further comprising crossing the selectedfirst soybean plant or first soybean germplasm with a second soybeanplant or second soybean germplasm.11. The method of embodiment 10, wherein the second soybean plant orsecond soybean germplasm comprises an exotic soybean strain or an elitesoybean strain.12. The method of any one of embodiments 1-11, wherein the detectingcomprises amplifying at least one of said marker loci and detecting theresulting amplified marker amplicon.13. The method of embodiment 12, wherein the amplifying comprises:

a) admixing an amplification primer or amplification primer pair foreach marker locus being amplified with a nucleic acid isolated from thefirst soybean plant or the first soybean germplasm, wherein the primeror primer pair is complementary or partially complementary to a variantor fragment of the genomic locus comprising the marker locus, and iscapable of initiating DNA polymerization by a DNA polymerase using thesoybean nucleic acid as a template; and

b) extending the primer or primer pair in a DNA polymerization reactioncomprising a DNA polymerase and a template nucleic acid to generate atleast one amplicon.

14. The method of embodiment 13, wherein said method comprisesamplifying a variant or fragment of one or more polynucleotidescomprising SEQ ID NOs: 135, 136, 137, 138, 139, 140, 141, 142, 143, 144,145, 146, 147, 148, 149, 150, 151, 152, 153 or 154.15. The method of embodiment 13, wherein said primer or primer paircomprises a variant or fragment of one or more polynucleotidescomprising SEQ ID NOs: 135, 136, 137, 138, 139, 140, 141, 142, 143, 144,145, 146, 147, 148, 149, 150, 151, 152, 153, 154, or complementsthereof.16. The method of embodiment 15, wherein said primer or primer paircomprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 or variants or fragmentsthereof.17. The method of embodiment 16, wherein said primer pair comprises:

a) SEQ ID NO: 1 and SEQ ID NO:2;

b) SEQ ID NO: 8 and SEQ ID NO:9;

c) SEQ ID NO: 10 and SEQ ID NO:13;

d) SEQ ID NO: 18 and SEQ ID NO:19;

e) SEQ ID NO: 31 and SEQ ID NO:32;

f) SEQ ID NO: 39 and SEQ ID NO:40;

g) SEQ ID NO: 50 and SEQ ID NO:51;

h) SEQ ID NO: 64 and SEQ ID NO:65; or

i) SEQ ID NO: 66 and SEQ ID NO:67.

18. The method of embodiment 13, wherein said method comprisesamplifying a variant or fragment of SEQ ID NOs: 155 or 156.19. The method of embodiment 13, wherein said primer or primer paircomprises a variant or fragment of SEQ ID NOs: 155, 156 or complementsthereof.20. The method of embodiment 19, wherein said primer or primer paircomprises a nucleic acid sequence comprising SEQ ID NOs: 72, 73, 74, 75,76, 77, 78, 79, 80, 81 or variants or fragments thereof.21. The method of embodiment 20, wherein said primer pair comprises SEQID NO: 72 or SEQ ID NO: 73.22. The method of embodiment 13, wherein said method comprisesamplifying a variant or fragment of SEQ ID NOs: 157 or 158.23. The method of embodiment 13, wherein said primer or primer paircomprises a variant or fragment of SEQ ID NOs: 157, 158 or complementsthereof.24. The method of embodiment 23, wherein said primer or primer paircomprises a nucleic acid sequence comprising SEQ ID NOs: 82, 83, 84, 85,86 or variants or fragments thereof.25. The method of embodiment 23, wherein said primer pair comprises SEQID NO: 82 and SEQ ID NO: 83.26. The method of embodiment 13, wherein the method further comprisesproviding one or more labeled nucleic acid probes suitable for detectionof each marker locus being amplified.27. The method of embodiment 26, wherein said labeled nucleic acid probecomprises a nucleic acid sequence comprising a variant or fragment ofone or more polynucleotides comprising SEQ ID NOs: 135, 136, 137, 138,139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,153, 154 or complements thereof.28. The method of embodiment 27, wherein the labeled nucleic acid probecomprises a nucleic acid sequence comprising SEQ ID NOs: 87, 88, 89, 90,91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105 or 106.29. The method of embodiment 26, wherein said labeled nucleic acid probecomprises a nucleic acid sequence comprising a variant or fragment ofSEQ ID NOs: 155, 156 or complements thereof.30. The method of embodiment 29, wherein the labeled nucleic acid probecomprises a nucleic acid sequence comprising SEQ ID NOs: 107 or 108.31. The method of embodiment 26, wherein said labeled nucleic acid probecomprises a nucleic acid sequence comprising a variant or fragment ofSEQ ID NOs: 157, 158 or complements thereof.32. The method of embodiment 31, wherein the labeled nucleic acid probecomprises a nucleic acid sequence comprising SEQ ID NOs: 109 or 110.33. The method of any one of embodiments 1-7, wherein the detectingcomprises DNA sequencing of at least one of said marker loci.34. An isolated polynucleotide capable of detecting a marker locus ofthe soybean genome comprising S04196-1-B, S04938-1-A, S04937-1-Q1,S08344-1-Q1, S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1,S04197-1 or a marker closely linked thereto.35. The isolated polynucleotide of embodiment 34, wherein thepolynucleotide comprises:

(a) a polynucleotide comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,64, 65, 66, 67, 68, 69, 70 or 71;

(b) a polynucleotide comprising SEQ ID NOs: 87, 88, 89, 90, 91, 92, 93,94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105 or 106;

(c) a polynucleotide having at least 90% sequence identity to thepolynucleotides set forth in parts (a) or (b); or

(d) a polynucleotide comprising at least 10 contiguous nucleotides ofthe polynucleotides set forth in parts (a) or (b).

36. An isolated polynucleotide capable of detecting a marker locus ofthe soybean genome comprising S07162-1-Q1 or a marker closely linkedthereto.37. The isolated polynucleotide of embodiment 36, wherein thepolynucleotide comprises:

(a) a polynucleotide comprising SEQ ID NOs: 72, 73, 74, 75, 76, 77, 78,79, 80 or 81;

(b) a polynucleotide comprising SEQ ID NOs: 107 or 108;

(c) a polynucleotide having at least 90% sequence identity to thepolynucleotides set forth in parts (a) or (b); or

(d) a polynucleotide comprising at least 10 contiguous nucleotides ofthe polynucleotides set forth in parts (a) or (b).

38. An isolated polynucleotide capable of detecting a marker locus ofthe soybean genome comprising S07161-1-Q1 or a marker closely linkedthereto.39. The isolated polynucleotide of embodiment 38, wherein thepolynucleotide comprises:

(a) a polynucleotide comprising SEQ ID NOs: 82, 83, 84, 85 or 86;

(b) a polynucleotide comprising SEQ ID NOs: 109 or 110;

(c) a polynucleotide having at least 90% sequence identity to thepolynucleotides set forth in parts (a) or (b); or

(d) a polynucleotide comprising at least 10 contiguous nucleotides ofthe polynucleotides set forth in parts (a) or (b).

40. A kit for detecting or selecting at least one soybean plant orsoybean germplasm with improved resistance to soybean cyst nematode, thekit comprising:

a) primers or probes for detecting one or more marker loci associatedwith resistance to soybean cyst nematode, wherein the primers or probesare capable of detecting a marker locus, wherein:

-   -   (i) the marker locus is between about marker Sat_123 and about        marker Satt453 on linkage group B1;    -   (ii) the marker locus is between about marker Sat_207 and about        marker Satt713 on linkage group C1; or    -   (iii) the marker locus is between about marker Satt574 and about        marker Satt615 on linkage group D2; and

b) instructions for using the primers or probes for detecting the one ormore marker loci and correlating the detected marker loci with predictedresistance to soybean cyst nematode.

41. The kit of embodiment 40, wherein the primers or probes are capableof detecting a marker locus comprising

(a) S04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1, S08343-1-Q1,S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1 or a marker closelylinked thereto;

(b) S07162-1-Q1 or a marker closely linked thereto; or

(c) S07161-1-Q1 or a marker closely linked thereto.

42. A method of identifying a first soybean plant or a first soybeangermplasm that displays improved resistance to soybean cyst nematode,the method comprising detecting in the genome of said first soybeanplant or in the genome of said first soybean germplasm at least onemarker locus that is associated with the resistance, wherein:

-   -   (a) the at least one marker locus is flanked by marker locus        S00875 and S02621 on linkage group D1b;    -   (b) the at least one marker locus is flanked by marker locus        S00479 and S02136 on linkage group D1b;    -   (c) the at least one marker locus is flanked by marker locus        Sat_264 and BARC-020449-04623 on linkage group B2;    -   (d) the at least one marker locus is flanked by marker locus        S02874 and S04785 on linkage group B2;    -   (e) the at least one marker locus is flanked by marker locus        S04348 and S01999 on linkage group B1;    -   (f) the at least one marker locus is flanked by marker locus        S01209 and S01999 on linkage group B1;    -   (g) the at least one marker locus is flanked by marker locus        Satt557 and Satt307 on linkage group C2;    -   (h) the at least one marker locus is flanked by marker locus        S03252 and S02112 on linkage group C2; or,    -   (i) the at least one marker locus comprises S00350-1-A,        S02183-1-A, or a marker closely linked thereto; or,    -   (j) the at least one marker locus is flanked by marker locus        S02074 and S03991 on linkage group L.        43. The method of embodiment 42, wherein the at least one marker        locus of part (a) comprises S01519-1-A, S08177-1-Q1, S00479-1-A,        S02136-1-A, S00875-1-A, S12875-1-Q1, S12950-1-Q1, S12947-1-Q1,        S12933-1-Q1, S12853-1-Q1, S03246-1-A, S12962-1-Q1 S00144-1-A,        S08166-1-Q1, S01081, and, S02621-1-A or a marker closely linked        thereto.        44. The method of embodiment 42, wherein the at least one marker        locus of part (c) comprises S02874-1-A, S04785-1-A, or a marker        closely linked thereto.        45. The method of embodiment 42, wherein the at least one marker        locus of part (e) comprises S04348-1-A, S01209-1-A, S01999-1-A,        or a marker closely linked thereto.        46. The method of embodiment 42, wherein the at least one marker        locus of part (f) comprises S04937-2-A, S04937-1-Q1, S04938-1-A,        S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1, S06787-2-Q1,        S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1, S06805-1-Q1,        S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, or        S06792-1-Q1 or a marker closely linked thereto.        47. The method of embodiment 42, wherein the at least one marker        locus of part (g) comprises S03252-1-A, S02112-1-A, or a marker        closely linked thereto.        48. The method of embodiment 42, wherein the at least one marker        locus of part (j) comprises S02074-1-A, S03991-1-A, or a marker        closely linked thereto.        49. The method of any one of embodiments 42-48, wherein at least        two marker loci are detected.        50. The method of any one of embodiments 42-49, wherein the        germplasm is a soybean variety.        51. The method of any one of embodiments 42-50, wherein the        method further comprises selecting the first soybean plant or        first soybean germplasm or a progeny thereof having the at least        one marker locus.        52. The method of embodiment 51, further comprising crossing the        selected first soybean plant or first soybean germplasm with a        second soybean plant or second soybean germplasm.        53. The method of embodiment 52, wherein the second soybean        plant or second soybean germplasm comprises an exotic soybean        strain or an elite soybean strain.        54. The method of any one of embodiments 42-51, wherein the        detecting comprises amplifying at least one of said marker loci        and detecting the resulting amplified marker amplicon.        55. The method of embodiment 54, wherein the amplifying        comprises:    -   a) admixing an amplification primer or amplification primer pair        for each marker locus being amplified with a nucleic acid        isolated from the first soybean plant or the first soybean        germplasm, wherein the primer or primer pair is complementary or        partially complementary to a variant or fragment of the genomic        locus comprising the marker locus, and is capable of initiating        DNA polymerization by a DNA polymerase using the soybean nucleic        acid as a template; and    -   b) extending the primer or primer pair in a DNA polymerization        reaction comprising a DNA polymerase and a template nucleic acid        to generate at least one amplicon.        56. The method of embodiment 55, wherein said method comprises        amplifying a variant or fragment of one or more polynucleotides        comprising SEQ ID NOs: 339, 340, 341, 342, 343, 344, 345, 346,        347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359,        360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372,        373, 374, 375, 376, and/or 377.        57. The method of embodiment 55, wherein said primer or primer        pair comprises a variant or fragment of one or more        polynucleotides comprising SEQ ID NOs: 339, 340, 341, 342, 343,        344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356,        357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369,        370, 371, 372, 373, 374, 375, 376, and/or 377 or complements        thereof.        58. The method of embodiment 57, wherein said primer or primer        pair comprises a nucleic acid sequence comprising SEQ ID NOs:        159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171,        172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184,        185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197,        198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210,        211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,        224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236,        237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, and/or        248 or variants or fragments thereof        59. The method of embodiment 58, wherein said primer pair        comprises the pairs as shown in Table 3.        60. The method of embodiment 55, wherein the method further        comprises providing one or more labeled nucleic acid probes        suitable for detection of each marker locus being amplified.        61. The method of embodiment 60, wherein said labeled nucleic        acid probe comprises a nucleic acid sequence comprising a        variant or fragment of one or more polynucleotides comprising        SEQ ID NOs: 339, 340, 341, 342, 343, 344, 345, 346, 347, 348,        349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361,        362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374,        375, 376, and/or 377 or complements thereof.        62. The method of embodiment 61, wherein the labeled nucleic        acid probe comprises a nucleic acid sequence comprising SEQ ID        NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260,        261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,        274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,        287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299,        300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312,        313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325,        326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337,        and/or 338.        63. The method of any one of embodiments 41-53, wherein the        detecting comprises DNA sequencing of at least one of said        marker loci.        64. An isolated polynucleotide capable of detecting a marker        locus of the soybean genome comprising    -   a) S00350-1-A, S02183-1-A, or a marker closely linked thereto;    -   b) S01519-1-A, S08177-1-Q1, S00479-1-A, S02136-1-A, S00875-1-A,        S12875-1-Q1, S12950-1-Q1, S12947-1-Q1, S12933-1-Q1, S12853-1-Q1,        S03246-1-A, S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081,        S02621-1-A or a marker closely linked thereto;    -   c) S02874-1-A, S04785-1-A, or a marker closely linked thereto;    -   d) S04348-1-A, S01209-1-A, S01999-1-A, or a marker closely        linked thereto;    -   e) S04937-2-A, S04937-1-Q1, S04938-1-A, S04938-2-A, S06786-2-Q1,        S06786-3-Q1, S06786-1-Q1, S06787-2-Q1, S06787-1-Q1, S06803-1-Q1,        S06804-1-Q1, S06788-1-Q1, S06805-1-Q1, S06789-1-Q1, S06790-1-Q1,        S06791-2-Q1, S06791-1-Q1, or S06792-1-Qlor a marker closely        linked thereto;    -   f) S03252-1-A, S02112-1-A, or a marker closely linked thereto;        or,    -   g) S02074-1-A, S03991-1-A, or a marker closely linked thereto.        65. The isolated polynucleotide of embodiment 64, wherein the        polynucleotide comprises:    -   (a) a polynucleotide comprising SEQ ID NOs: 159, 160, 161, 162,        163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,        176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188,        189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201,        202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214,        215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227,        228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240,        241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253,        254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266,        267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279,        280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292,        293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305,        306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318,        319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,        332, 333, 334, 335, 336, 337, and/or 338;    -   (b) a polynucleotide having at least 90% sequence identity to        the polynucleotides set forth in part (a); or    -   (d) a polynucleotide comprising at least 10 contiguous        nucleotides of the polynucleotides set forth in part (a).        66. A kit for detecting or selecting at least one soybean plant        or soybean germplasm with improved resistance to soybean cyst        nematode, the kit comprising:    -   a) a primer or a probe for detecting one or more marker loci        associated with resistance to soybean cyst nematode, wherein the        primer or probe are capable of detecting a marker locus,        wherein:        -   (i) the at least one marker locus is flanked by marker locus            S00875 and S02621 on linkage group D1b;        -   (ii) the at least one marker locus is flanked by marker            locus S00479 and S02136 on linkage group D1b;        -   (iii) the at least one marker locus is flanked by marker            locus Sat_264 and BARC-020449-04623 on linkage group B2;        -   (iv) the at least one marker locus is flanked by marker            locus S02874 and S04785 on linkage group B2;        -   (v) the at least one marker locus is flanked by marker locus            S04348 and S01999 on linkage group B1;        -   (vi) the at least one marker locus is flanked by marker            locus S01209 and S01999 on linkage group B1;        -   (vii) the at least one marker locus is flanked by marker            locus Satt557 and Satt307 on linkage group C2;        -   (viii) the at least one marker locus is flanked by marker            locus S03252 and S02112 on linkage group C2; or,        -   (iix) the at least one marker locus comprises S00350-1-A,            S02183-1-A, or a marker closely linked thereto; or,        -   (ix) the at least one marker locus is flanked by marker            locus S02074 and S03991 on linkage group L; and,    -   b) instructions for using the primers or probes for detecting        the one or more marker loci and correlating the detected marker        loci with predicted resistance to soybean cyst nematode.        67. The kit of embodiment 66, wherein the primer or probe is        capable of detecting a marker locus comprising

(a) the at least one marker locus comprises S01519-1-A, S08177-1-Q1,S00479-1-A, S02136-1-A, S00875-1-A, S12875-1-Q1, S12950-1-Q1,S12947-1-Q1, S12933-1-Q1, S12853-1-Q1, S03246-1-A, S12962-1-Q1S00144-1-A, S08166-1-Q1, S01081, S02621-1-A or a marker closely linkedthereto;

(b) the at least one marker locus comprises S02874-1-A, S04785-1-A, or amarker closely linked thereto;

(c) the at least one marker locus comprises S04348-1-A, S01209-1-A,S01999-1-A, or a marker closely linked thereto;

(d) the at least one marker locus comprises S04937-2-A, S04937-1-Q1,S04938-1-A, S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1,S06787-2-Q1, S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1,S06805-1-Q1, S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, orS06792-1-Qlor a marker closely linked thereto;

(e) the at least one marker locus of part (g) comprises S03252-1-A,S02112-1-A, or a marker closely linked thereto.

(f) the at least one marker locus of part (j) comprises S02074-1-A,S03991-1-A, or a marker closely linked thereto.

EXPERIMENTAL

The following examples are offered to illustrate, but not to limit theclaimed invention. It is understood that the examples and embodimentsdescribed herein are for illustrative purposes only, and persons skilledin the art will recognize various reagents or parameters that can bealtered without departing from the spirit of the invention or the scopeof the appended claims.

Example 1

Markers were developed to characterize, identify, and/or selectresistant or susceptible alleles at the SCN loci on linkage groups B1,C1 and D2. Markers were screened against various known resistant andsusceptible parents.

During development, these markers were validated and confirmed against apanel of 31 varieties which included proprietary experimental lines,proprietary commercial lines, and public lines.

TABLE 11 Assay conditions: H20  4.28 ul Hot Tub buffer  0.5 ul Rox Dye(50X) 0.075 ul DNTPs (24 mM each) 0.039 ul Primer (100 uM) 0.0375 ul Primer (100 uM) 0.0375 ul  Primer (100 uM) 0.0375 ul  FAM Probe (100 uM0.005 ul VIC Probe (100 uM 0.005 ul Hot Tub enzyme 0.025 ul Total volume5.005 ul

Further development and testing was done to optimize the markercomponents for high throughput analysis of soybean. From this testing,an optimal set of primer and probe combinations were chosen for highthroughput analysis needs, but other versions can be used to detect thepolymorphism(s) associated with the phenotype.

Similar development, testing and analysis was done to produce anyadditional markers to detect polymorphisms associated with theidentified SCN loci and soybean cyst nematode resistance, with theresults of this work summarized in the Tables provided herein. Themarkers were validated against the panel of SCN resistant or susceptiblevarieties described above. The markers are capable of detecting SCN locilikely derived from one or more of PI88788, Peking, PI437654, as wellmarkers from other sources. These markers may have further beenoptimized for robust and consistent performance in high throughput assayconditions.

These markers can be used in other assays or with other assayconditions. Some markers were assayed under additional conditions, anexample of which is summarized below.

The parameters used for the TaqMan assay are as follows in Table 12 and13.

TABLE 12 Cycle Settings 94° C. 120 sec   1 cycle 60° C. 60 sec 40 cycles72° C.  1 sec 94° C. 30 sec

TABLE 13 Assay Mix 1x (ul) DNA (1.5 ng) - dried down in assay plate —ddH₂0 3.95 Hottub buffer 0.5 dNTP (2.5 mM) 0.375 Primer 1 + Primer 2(100 uM F + R) 0.02 Probe 1 (10 uM) 0.05 Probe 2 (10 uM) 0.05 Hottubenzyme 0.025 Rox dye (50x) 0.075 Total 5.05

TABLE 14 Summary of SEQ ID NOs. Linkage SEQ ID NO Description Group 1Primer 141527 B1 2 Primer 141528 B1 3 Primer S4196-F2 B1 4 PrimerS4196-R2 B1 5 Primer S4196-F3 B1 6 Primer S4196-R3 B1 7 Primer S4196-R4B1 8 Primer S04938-F1 B1 9 Primer S04938-R1 B1 10 Primer 141535,S04937-F1 B1 11 Primer 141536 B1 12 Primer 148638, S04937-F5 B1 13Primer 148639, S04937-R3 B1 14 Primer S04937-F3 B1 15 Primer S04937-F4B1 16 Primer S04937-R4 B1 17 Primer S04937-R5 B1 18 Primer 136830 B1 19Primer 136831 B1 20 Primer P12198A1-F (128-) 76806 B1 21 Primer 86074:P12198A-1T66A218F B1 22 Primer 86075: P12198A-1T66A218R B1 23 Primer92472-p12198A1_R B1 24 Primer 136828 B1 25 Primer 136829 B1 26 Primer136832 B1 27 Primer 136833 B1 28 Primer 19661 B1 29 Primer 19389 B1 30Primer 96347 B1 31 Primer 136886 B1 32 Primer 136887 B1 33 PrimerP8584A-1-F2, 82593 B1 34 Primer Reverse primer 15081 B1 35 Primer 136884B1 36 Primer 136885 B1 37 Primer 136888 B1 38 Primer 136889 B1 39 Primer144687 B1 40 Primer 144688 B1 41 Primer S06786-1-Q1F B1 42 PrimerS06786-1-Q1R B1 43 Primer S06786-1-Q2R B1 44 Primer S06786-1-Q3F B1 45Primer S06786-1-Q3R B1 46 Primer S06786-1-Q4F B1 47 Primer S06786-1-Q4RB1 48 Primer S06786-1-Q5F B1 49 Primer S06786-1-Q5R B1 50 Primer 142755B1 51 Primer 142756 B1 52 Primer 142759 B1 53 Primer 142760 B1 54 PrimerS06787-1-Q2F B1 55 Primer S06787-1-Q2R B1 56 Primer S06787-1-Q3R B1 57Primer S06787-1-Q4F B1 58 Primer S06787-1-Q4R B1 59 Primer S06803-1-Q1FB1 60 Primer S06803-1-Q1R B1 61 Primer S06803-1-Q2F B1 62 PrimerS06803-1-Q3F B1 63 Primer S06803-1-Q3R B1 64 Primer 142386 B1 65 Primer142387 B1 66 Primer S04197-1-F2 B1 67 Primer S04197-1-R2 B1 68 PrimerS04197-1-F3 B1 69 Primer S04197-1-R3 B1 70 Primer S04197-1-F4 B1 71Primer S04197-1-R4 B1 72 Primer 136849 C1 73 Primer 136850 C1 74 Primer80907 C1 75 Primer 80908 C1 76 Primer 87501 C1 77 Primer 87504 C1 78Primer 136845 C1 79 Primer 136846 C1 80 Primer 136847 C1 81 Primer136848 C1 82 Primer 137370 D2 83 Primer 137374 D2 84 Primer 137371 D2 85Primer 137372 D2 86 Primer 137373 D2 87 Probe 141540 B1 88 Probe 141539B1 89 Probe S04938-1-P1 B1 90 Probe S04938-1-P2 B1 91 Probe 141537 B1 92Probe 141538 B1 93 Probe 102404 B1 94 Probe 102405 B1 95 Probe 102406 B196 Probe 102407 B1 97 Probe 102384 B1 98 Probe 102385 B1 99 Probe 142753B1 100 Probe 142754 B1 101 Probe 142757 B1 102 Probe 142758 B1 103 Probe142761 B1 104 Probe 142762 B1 105 Probe 142389 B1 106 Probe 142388 B1107 Probe 102396 C1 108 Probe 102397 C1 109 Probe 125316 D2 110 Probe125331 D2 111 Amplicon for S04196-1-B comprising resistance allele B1112 Amplicon for S04196-1-B comprising susceptible allele B1 113Amplicon for S04938-1-A comprising resistance allele B1 114 Amplicon forS04938-1-A comprising susceptible allele B1 115 Amplicon for S04937-1-Q1comprising resistance allele B1 116 Amplicon for S04937-1-Q1 comprisingsusceptible allele B1 117 Amplicon for S08344-1-Q1 comprising resistanceallele B1 118 Amplicon for S08344-1-Q1 comprising susceptible allele B1119 Amplicon for S08343-1-Q1 comprising resistance allele B1 120Amplicon for S08343-1-Q1 comprising susceptible allele B1 121 Ampliconfor S08346-1-Q1 comprising resistance allele B1 122 Amplicon forS08346-1-Q1 comprising susceptible allele B1 123 Amplicon for S06786-1comprising resistance allele B1 124 Amplicon for S06786-1 comprisingsusceptible allele B1 125 Amplicon for S06787-1 comprising resistanceallele B1 126 Amplicon for S06787-1 comprising susceptible allele B1 127Amplicon for S06803-1 comprising resistance allele B1 128 Amplicon forS06803-1 comprising susceptible allele B1 129 Amplicon for S04197-1comprising resistance allele B1 130 Amplicon for S04197-1 comprisingsusceptible allele B1 131 Amplicon for S07162-1-Q1comprising resistanceallele C1 132 Amplicon for S07162-1-Q1comprising susceptible allele C1133 Amplicon for S07161-1-Q1comprising resistance allele D2 134 Ampliconfor S07161-1-Q1comprising susceptible allele D2 135 Reference sequencefor S04196-1-B comprising resistance allele B1 136 Reference sequencefor S04196-1-B comprising susceptible allele B1 137 Reference sequencefor S04938-1-A comprising resistance allele B1 138 Reference sequencefor S04938-1-A comprising susceptible allele B1 139 Reference sequencefor S04937-1-Q1 comprising resistance allele B1 140 Reference sequencefor S04937-1-Q1 comprising susceptible allele B1 141 Reference sequencefor S08344-1-Q1 comprising resistance allele B1 142 Reference sequencefor S08344-1-Q1 comprising susceptible allele B1 143 Reference sequencefor S08343-1-Q1 comprising resistance allele B1 144 Reference sequencefor S08343-1-Q1 comprising susceptible allele B1 145 Reference sequencefor S08346-1-Q1 comprising resistance allele B1 146 Reference sequencefor S08346-1-Q1 comprising susceptible allele B1 147 Reference sequencefor S06786-1 comprising resistance allele B1 148 Reference sequence forS06786-1 comprising susceptible allele B1 149 Reference sequence forS06787-1 comprising resistance allele B1 150 Reference sequence forS06787-1 comprising susceptible allele B1 151 Reference sequence forS06803-1 comprising resistance allele B1 152 Reference sequence forS06803-1 comprising susceptible allele B1 153 Reference sequence forS04197-1 comprising resistance allele B1 154 Reference sequence forS04197-1 comprising susceptible allele B1 155 Reference sequence forS07162-1-Q1comprising resistance allele C1 156 Reference sequence forS07162-1-Q1comprising susceptible allele C1 157 Reference sequence forS07161-1-Q1comprising resistance allele D2 158 Reference sequence forS07161-1-Q1comprising susceptible allele D2

Example 2 Materials and Methods

Population:

Three different homozygous PI90763-derived donor parents were used tocreate three backcross populations, consisting of five replicates of 92,83, and 69 progeny, respectively. The respective family names for thepopulations are LP40401802 (1802), LP40401803 (1803), and LP40401805(1805). Six punches from separate plants were sampled per line andsubmitted for genotyping as JB29911. The plates were CTAB extracted toisolate DNA for analysis.

Genotyping:

The putative QTL region on linkage group D1b_(2) was saturated with 16polymorphic markers for genotyping

Phenotyping:

SCN2 scores (1-9 scale) were provided for each replication of each lineand the scores were averaged to give one score per line. A haplotypeanalysis of the D1b region and the results were used to divide theprogeny into a recombinant data set and a non-recombinant data set.

QTL Analysis:

Single marker analysis was executed using QTL Cartographer 2.5 (Wang etal. (2011) Windows QTL Cartographer 2.5; Dept. of Statistics, NorthCarolina State University, Raleigh, N.C. Available online atstatgen.ncsu.edu/qticart/WQTLCart.htm).

Results:

Genotyping:

Three markers were removed from all three families that were segregatingbetween the two susceptible parents, one monomorphic marker was removedfrom family 1802, and two monomorphic markers were removed from family1805. The remaining allele calls were converted to the A (maternal), B(paternal), H (heterozygous) convention for QTL analysis.

The segregation ratios among the three families varied widely withfamily 1802 skewed towards the susceptible parents, 1803 skewed towardsthe resistant parent, and 1805 fairly equal

Phenotyping:

The phenotypic distributions for the populations were evaluated witheachline represented once using the average score across samples. Eachpopulation was evaluated as a whole and then broken down into arecombinant data set and a non-recombinant data set (family 1803 progenywere all classified as recombinant). The average SCN2 score for theparents are as follows: Parent 1=3.0, Parent 2=2.2, and PI090763=8.4.

Single Marker Analysis:

Highly significant markers associated with SCN were found on Lg-D1b.Single marker analysis was conducted for each family and then thefamilies were broken down into recombinant and non-recombinant groupsand the analysis was repeated. The tables below show the markers foundto be significant at a pr(F)<0.05, and the markers/intervals of highestsignificance are indicated in bold for each set.

Family LP40401802:

No highly significant associations were identified in family 1802. Thehighest significance was found in the non-recombinant data set at markerS00479-1-A (91.61 cM), explaining 24% of the variation. Minorsignificance was found at marker S01519-1-A across all progeny and inthe recombinant data set, explaining 11% of the variation.

TABLE 15 Family Data Set Marker LG LRS pr(F) R2 LP40401802 All progenyS00479-1-A D1b_(2) 3.966 0.04957 0.046 LP40401802 All progeny S00875-1-AD1b_(2) 6.084 0.01501 0.065 LP40401802 All progeny S12947-1-Q1 D1b_(2)6.084 0.01501 0.065 LP40401802 All progeny S12933-1-Q1 D1b_(2) 9.3040.00263 0.087 LP40401802 All progeny S01519-1-A D1b_(2) 10.743 0.001230.113 LP40401802 All progeny S08177-1-Q1 D1b_(2) 6.986 0.00916 0.074LP40401802 Non-recombinant S00479-1-A D1b_(2) 9.310 0.00324 0.239LP40401802 Non-recombinant S01519-1-A D1b_(2) 4.478 0.04120 0.117LP40401802 Recombinant S12933-1-Q1 D1b_(2) 5.166 0.02643 0.083LP40401802 Recombinant S01519-1-A D1b_(2) 6.316 0.01411 0.110 LP40401802Recombinant S08177-1-Q1 D1b_(2) 4.278 0.04338 0.075 LRS = likelihoodratio statistic. pr(F) is the F test statistic testing the nullhypothesis. 0.05 is the lowest level of significance, anything <0.0001is highly significant.

Family LP40401803:

Significance was found in family 1803 between markers S00875-1-A (113.96cM) and S12933-1-Q1 (cM), explaining 15% of the variation. Norecombination was observed in this interval.

TABLE 16 Family Data Set Marker LG LRS pr(F) R2 LP40401803 RecombinantS02136-1-A D1b_(2) 4.731 0.03236 0.059 LP40401803 Recombinant S00875-1-AD1b_(2) 12.686 0.00046 0.150 LP40401803 Recombinant S12875-1-Q1 D1b_(2)11.423 0.00088 0.125 LP40401803 Recombinant S12950-1-Q1 D1b_(2) 12.6860.00046 0.150 LP40401803 Recombinant S12947-1-Q1 D1b_(2) 12.037 0.000640.137 LP40401803 Recombinant S12933-1-Q1 D1b_(2) 12.686 0.00046 0.150LP40401803 Recombinant S12853-1-Q1 D1b_(2) 10.248 0.00163 0.119LP40401803 Recombinant S03246-1-A D1b_(2) 10.744 0.00126 0.129LP40401803 Recombinant S12962-1-Q1 D1b_(2) 7.494 0.00707 0.092LP40401803 Recombinant S08177-1-Q1 D1b_(2) 8.056 0.00523 0.098

Family LP40401805:

Highly significant markers were found in family 1805 between markersS12875-1-Q1 (cM) and S12933-1-Q1 (cM), explaining 31% of the variationusing all progeny and 18% of the variation using only recombinantprogeny. No recombination was observed in this interval. Significancewas not found using the non-recombinant data set.

TABLE 17 Family Data Set Marker LG LRS pr(F) R2 LP40401805 All progenyS02136-1-A D1b_(2) 4.158 0.04537 0.059 LP40401805 All progeny S00875-1-AD1b_(2) 11.254 0.00099 0.153 LP40401805 All progeny S12875-1-Q1 D1b_(2)24.834 0.00000 0.304 LP40401805 All progeny S12950-1-Q1 D1b_(2) 24.8340.00000 0.306 LP40401805 All progeny S12947-1-Q1 D1b_(2) 24.129 0.000000.299 LP40401805 All progeny S12933-1-Q1 D1b_(2) 24.129 0.00000 0.304LP40401805 All progeny S12853-1-Q1 D1b_(2) 22.994 0.00000 0.285LP40401805 All progeny S03246-1-A D1b_(2) 22.994 0.00000 0.287LP40401805 All progeny S01519-1-A D1b_(2) 22.377 0.00000 0.280LP40401805 Recombinant S12875-1-Q1 D1b_(2) 9.076 0.00339 0.179LP40401805 Recombinant S12950-1-Q1 D1b_(2) 9.076 0.00339 0.179LP40401805 Recombinant S12947-1-Q1 D1b_(2) 9.076 0.00339 0.179LP40401805 Recombinant S12933-1-Q1 D1b_(2) 9.076 0.00339 0.179LP40401805 Recombinant S12853-1-Q1 D1b_(2) 7.411 0.00811 0.149LP40401805 Recombinant S03246-1-A D1b_(2) 7.411 0.00811 0.149 LP40401805Recombinant S01519-1-A D1b_(2) 7.411 0.00811 0.149 LP40401805Recombinant S08177-1-Q1 D1b_(2) 7.075 0.00969 0.163Recombinant and non-recombinant haplotypes were identified in thesethree populations, and are summarized below in Table ??, wherer=resistant, h=heterozygous, and s=susceptible

TABLE 18 D1b Haplotype S00875 S01519 S00144 S01081 rrrr G C C C rrhh G CC, G A, C rrhs G C C, G A ssrr A T C C rrss G C G A hrrr A, G C C C rrrhG C C A, C hrrh A, G C C A, C rrrs G C C A rsrr G T C C srrr A C C Csssr A T G C srrh A C C A, C srsr A C G C

Example 3 Materials and Methods

Population:

The population LP40401802 comprised of 204 progeny replicated five timeseach, was submitted as JB15967 and CTAB extracted for genotyping.

Genotyping:

The putative QTL region on linkage group D1b (2) was saturated with 17polymorphic markers, with the rest of the chromosome covered by anadditional 13 markers. All marker selections were made using aproprietary software to select markers distributed across the linkagegroup.

Phenotyping:

Raw cyst counts and the derived 1-9 SCN2 scores were provided for eachof the 1020 progeny and parental samples. The scores were averaged foreach variety, resulting in 204 progeny scores.

Linkage Analysis:

Map Manager QTX.b20 was used for linkage map construction with thefollowing parameters:

1) Linkage Evaluation: Advanced Backcross 2

2) Search Criteria: P=1e⁻⁵

3) Map Function: Haldane

4) Cross Type: Line Cross

QTL Analysis:

Single marker analysis and composite interval mapping (CIM) wereexecuted using QTL Cartographer 2.5. The standard CIM model and forwardand backward regression method was used, and the LRS threshold forstatistical significance was set to the default value of 11.5.

Results:

Genotyping:

A consensus call was calculated for each variety and then converted tothe A (maternal), B (paternal), H (heterozygous) convention for QTLanalysis. Three markers were removed from the analysis because thematernal call was heterozygous while Parent 2 and PI90763 werehomozygous for opposite alleles. An additional marker was removed thatfailed genotyping.

Phenotyping:

The phenotypic distributions were evaluated using an average scoreacross samples for eachline. The population was evaluated as a whole andthen broken down into a recombinant data set and a non-recombinant dataset.

Mapping Analysis:

Linkage mapping was performed in Map Manager QTX.b20 using AdvancedBackcross 2 for the Linkage Evaluation setting.

Single Marker Analysis:

Single marker analysis was performed using all 204 progeny, 107recombinant progeny, and 97 non-recombinant progeny for both the rawcyst counts and SCN2 scores. Highly significant markers were observed atthe p=0.0001 level using all progeny and recombinant progeny across bothdata setsThe non-recombinant data set identified peak markers in asimilar area, but showed less significance (p=0.001 level). Allsignificant markers among the data sets have effects coming fromPI90763.

TABLE 19 Chrom LRS F(1, n − 2) pr(F) R2 S00479-1-A D1b_(2) 7.605 7.6720.00613 0.037 S00875-1-A D1b_(2) 31.354 33.560 0.00000 0.143 S12875-1-Q1D1b_(2) 39.481 43.133 0.00000 0.176 S12950-1-Q1 D1b_(2) 38.950 42.4970.00000 0.174 S12947-1-Q1 D1b_(2) 39.800 43.517 0.00000 0.177S12933-1-Q1 D1b_(2) 41.250 45.268 0.00000 0.183 S12853-1-Q1 D1b_(2)27.427 29.068 0.00000 0.126 S03246-1-A D1b_(2) 27.567 29.227 0.000000.126 S01519-1-A D1b_(2) 14.907 15.314 0.00012 0.071 S12962-1-Q1 D1b_(2)3.521 3.517 0.06218 0.017 S00144-1-A D1b_(2) 3.441 3.436 0.06525 0.017S08166-1-Q1 D1b_(2) 3.251 3.245 0.07313 0.016 S01081-1-A D1b_(2) 0.2980.295 0.58775 0.002

TABLE 20 Marker Chrom LRS F(1, n − 2) pr(F) R2 S00479-1-A D1b_(2) 8.5338.628 0.00369 0.041 S00875-1-A D1b_(2) 32.327 34.686 0.00000 0.147S12875-1-Q1 D1b_(2) 40.357 44.188 0.00000 0.180 S12950-1-Q1 D1b_(2)39.963 43.713 0.00000 0.178 S12947-1-Q1 D1b_(2) 40.689 44.589 0.000000.181 S12933-1-Q1 D1b_(2) 42.131 46.339 0.00000 0.187 S12853-1-Q1D1b_(2) 28.012 29.732 0.00000 0.128 S03246-1-A D1b_(2) 28.112 29.8450.00000 0.129 S01519-1-A D1b_(2) 14.376 14.749 0.00016 0.068 S12962-1-Q1D1b_(2) 3.272 3.266 0.07222 0.016 S00144-1-A D1b_(2) 3.161 3.154 0.077230.015 S08166-1-Q1 D1b_(2) 3.039 3.032 0.08318 0.015 S01081-1-A D1b_(2)0.263 0.260 0.61043 0.001

TABLE 21 Marker Chrom LRS F(1, n − 2) pr(F) R2 S00479-1-A D1b_(2) 7.6447.776 0.00629 0.069 S00875-1-A D1b_(2) 28.525 32.078 0.00000 0.234S12875-1-Q1 D1b_(2) 38.096 44.905 0.00000 0.300 S12950-1-Q1 D1b_(2)38.096 44.905 0.00000 0.300 S12947-1-Q1 D1b_(2) 37.891 44.618 0.000000.298 S12933-1-Q1 D1b_(2) 41.134 49.222 0.00000 0.319 S12853-1-Q1D1b_(2) 24.658 27.212 0.00000 0.206 S03246-1-A D1b_(2) 26.949 30.0740.00000 0.223 S01519-1-A D1b_(2) 1.731 1.713 0.19349 0.016 S12962-1-Q1D1b_(2) 4.397 4.405 0.03823 0.040 S00144-1-A D1b_(2) 4.271 4.276 0.041110.039 S08166-1-Q1 D1b_(2) 4.397 4.405 0.03823 0.040 S01081-1-A D1b_(2)11.558 11.977 0.00078 0.102

TABLE 22 Marker Chrom LRS F(1, n − 2) pr(F) R2 S00479-1-A D1b_(2) 8.4028.577 0.00417 0.076 S00875-1-A D1b_(2) 30.332 34.412 0.00000 0.247S12875-1-Q1 D1b_(2) 39.829 47.352 0.00000 0.311 S12950-1-Q1 D1b_(2)39.829 47.352 0.00000 0.311 S12947-1-Q1 D1b_(2) 39.480 46.856 0.000000.309 S12933-1-Q1 D1b_(2) 42.940 51.847 0.00000 0.331 S12853-1-Q1D1b_(2) 24.825 27.419 0.00000 0.207 S03246-1-A D1b_(2) 27.118 30.2870.00000 0.224 S01519-1-A D1b_(2) 1.411 1.394 0.24048 0.013 S12962-1-Q1D1b_(2) 4.729 4.744 0.03163 0.043 S00144-1-A D1b_(2) 4.647 4.660 0.033140.043 S08166-1-Q1 D1b_(2) 4.729 4.744 0.03163 0.043 S01081-1-A D1b_(2)11.842 12.288 0.00067 0.105

TABLE 23 Chrom LRS F(1, n − 2) pr(F) R2 D1b_(2) 1.159 1.142 0.287960.012 D1b_(2) 9.125 9.371 0.00287 0.090 D1b_(2) 11.664 12.138 0.000750.113 D1b_(2) 11.198 11.625 0.00096 0.109 D1b_(2) 11.961 12.467 0.000640.116 D1b_(2) 11.664 12.138 0.00075 0.113 D1b_(2) 8.358 8.549 0.004320.083 D1b_(2) 8.185 8.365 0.00474 0.081 D1b_(2) 9.935 10.246 0.001860.097 D1b_(2) 12.522 13.091 0.00048 0.121 D1b_(2) 12.230 12.766 0.000560.119 D1b_(2) 11.742 12.225 0.00072 0.114 D1b_(2) 10.448 10.804 0.001420.102

TABLE 24 Marker Chrom LRS F(1, n − 2) pr(F) R2 S00479-1-A D1b_(2) 1.4121.393 0.24078 0.015 S00875-1-A D1b_(2) 9.014 9.251 0.00304 0.089S12875-1-Q1 D1b_(2) 11.479 11.935 0.00083 0.112 S12950-1-Q1 D1b_(2)11.116 11.535 0.00100 0.108 S12947-1-Q1 D1b_(2) 11.826 12.318 0.000690.115 S12933-1-Q1 D1b_(2) 11.479 11.935 0.00083 0.112 S12853-1-Q1D1b_(2) 8.593 8.800 0.00381 0.085 S03246-1-A D1b_(2) 8.360 8.551 0.004320.083 S01519-1-A D1b_(2) 10.234 10.571 0.00159 0.100 S12962-1-Q1 D1b_(2)12.627 13.207 0.00045 0.122 S00144-1-A D1b_(2) 12.289 12.831 0.000540.119 S08166-1-Q1 D1b_(2) 11.900 12.400 0.00066 0.116 S01081-1-A D1b_(2)10.442 10.797 0.00142 0.102

Example 4

The goal of this study was to confirm the QTLs reported in the paper TAG(2005) 111:965—another F4 population from a biparental cross withP190763. This population has been previously phenotyped and an initialgenotyping job assayed 119 markers from the 7 chromosomes(Lg-A2/B1/E/G/J/L/O) reported as significant in the above literature.Marker regression significant associations on Lg-L and B1 (p=0.001), andinterval mapping also indicated Lg-L as significant. However, thechromosome positions of each QTL were inconsistent with the QTLpositions reported in the literature. In combination with a subsequentgenome-wide scan of the population (an additional 163 markers), a secondmapping analysis confirmed the minor QTL on Lg-L and indicated a majorQTL on Lg-D1b. The QTL on Lg-L was not consistent with the QTL reportedin the literature, while the QTL on Lg-D1b was not reported in eitherpaper. New phenotypic data was analyzed in this study using the previousgenotypic calls. A minor QTL was identified on Lg-B2, explaining 8% ofthe phenotypic variation, and the QTL on Lg-D1b was confirmed from theprior analysis, explaining 40% of the variation. When the first andsecond sets of phenotypic scores were averaged, one major and six minorQTLs were identified. The major QTL mapped to Lg-D1b in the intervalreported previously and explained 39% of the variation. Two minor QTLswere identified on Lg-B1, each explaining 7% of the phenotypicvariation, and one minor QTL was identified on each of Lg-C2, E, F, andL, explaining 7%, 8%, 10%, and 9% of the variation, respectively. WhileQTLs were identified on Lg-B1, E, and L in the literature, the positionsdo not seem consistent with the current findings.

Materials and Methods:

Population:

An F4 population from a biparental cross with PI90763 PI90763 consistingof 276 progeny was used for the study, PI90763 was the resistant donor.The tissue was lyophilized and submitted for genotyping as JB1048. Thetissue was then CTAB extracted to isolate DNA.

Genotyping:

Genotypic data from jobs J-D306 (119 markers) and J-G285 (163 markers)were employed in this analysis.

Phenotyping:

Phenotypic scores, ranged from a score of 1 (susceptible) to 9(resistant). The new data set was analyzed both alone (Set2_AVE) and asan average with the original data set (Total_AVE).

Linkage Analysis:

Map Manager QTX.b20 was used to construct the linkage map and performQTL analysis. The initial Map Manager Parameters were set to:

1) Linkage Evaluation: Intercross

2) Search Criteria: P=1e⁻⁵

3) Map Function: Kosambi

4) Cross Type: Line Cross

Genetic Map:

Preliminary analysis showed that 24 markers from J-G285 werenon-informative for QTL analysis due to the absence of a heterozygousclass. These markers were removed and the data for the remaining 139markers was combined with the data for 78 markers from J-D306. In all,45 markers showed segregation distortion but were retained in theanalysis. Allele calls for the 217 markers were then converted to the A(maternal), B (paternal), H (heterozygous) convention for QTL analysis.The 217 markers formed 48 linkage groups across the 20 chromosomes, with19 markers remaining unlinked. Marker arrangement was checked to ensurethe distorted markers linked as expected, and four markers were found tohave rearrangements. These were removed from the analysis.

Marker Regression Analysis:

Marker regression was performed (p=0.001) across all 217 markers,indicating significant associations on Lg-B2, D1b, E, L, and I in theSet2_AVE data set, and Lg-B1, C2, D1b, E, and L in the Total_AVE dataset.

A permutation test was run 1000 times using the free model, establishingthe threshold for statistical significance (LOD ratio statistic—LRS) todetermine putative QTL. LRS cutoffs were 11.0 for suggestive in Set2_AVEand total_AVE, 17.7 or 17.3 for significant in Set2_AVE and total_AVE,and 26.8 or 28.9 for highly significant in Set2_AVE and total_AVE.Interval mapping was performed using the bootstrap test, free regressionmodel, and the LRS cutoffs determined by the permutation test.

Set2_AVE: Major QTL on Lg-D1b, Minor QTL on Lg-B2

A major QTL was indicated near the bottom of Lg-D1b with a 1-LOD supportinterval of 3 cM between markers S01519-1-A and S02621-1-A and an LRS of131.6, explaining 40% of the phenotypic variation. A minor QTL was alsoindicated near the top of Lg-B2 at marker S02874-1-A with a 1-LODsupport interval of 3 cM between markers. The LRS was 21.1 and the QTLexplained 8% of the phenotypic variation.

Total_AVE: Major QTL on Lg-D1b, Six Minor QTL on Lg-B1, C2, E, and L

A major QTL was indicated near the bottom of Lg-D1b with a 1-LOD supportinterval of 3 cM between markers S01519-1-A and S02621-1-A and an LRS of131.1, explaining 39% of the phenotypic variation.

Two minor QTLs were identified about 28 cM apart in the top half ofLg-B1, each explaining 7% of the phenotypic variation. The first has a1-LOD support interval of 9 cM and LRS of 19.9. The second minor QTL hasa 1-LOD support interval of 5 cM between markers S01209-1-A andS01999-1-A and an LRS of 18.7.

A minor QTL was indicated near the bottom of Lg-C2 at marker S02112-1-A,This QTL had an LRS of 17.3, explaining 7% of the variation.

A minor QTL was identified near the bottom of Lg-E, highly associatedwith marker S02183-1-A and flanked to the north by S00350-1-A. Nomarkers were linked to the south. The QTL had an LRS of 20.2, explaining8% of the phenotypic variation.

A minor QTL was found at the top of Lg-L at marker S02074-1-A andflanked to the south by S03991-1-A. No markers were linked to the north.The QTL had an LRS of 20.7 and explained 9% of the phenotypic variation.

All publications and patent applications mentioned in the specificationare indicative of the level of those skilled in the art to which thisinvention pertains. All publications and patent applications are hereinincorporated by reference to the same extent as if each individualpublication or patent application was specifically and individuallyindicated to be incorporated by reference.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be obvious that certain changes and modificationsmay be practiced within the scope of the appended claims.

1. A method of identifying a first soybean plant or a first soybeangermplasm that displays improved resistance to soybean cyst nematode,the method comprising detecting in the genome of said first soybeanplant or in the genome of said first soybean germplasm at least onemarker locus that is associated with the resistance, wherein: the atleast one marker locus is between about marker Satt574 and about markerSatt615 on linkage group D2.
 2. The method of claim 1, wherein: the atleast one marker locus comprises S07161-1-Q1 or a marker closely linkedthereto.
 3. The method of claim 1, wherein at least two marker loci aredetected.
 4. The method of claim 3, wherein the at least two marker locicomprise a haplotype that is associated with said resistance.
 5. Themethod of claim 3, wherein the at least two marker loci comprise amarker profile that is associated with said resistance.
 6. The method ofclaim 1, wherein the germplasm is a soybean variety.
 7. The method ofclaim 1, wherein the method further comprises selecting the firstsoybean plant or first soybean germplasm or a progeny thereof having theat least one marker locus.
 8. The method of claim 7, further comprisingcrossing the selected first soybean plant or first soybean germplasmwith a second soybean plant or second soybean germplasm.
 9. The methodof claim 8, wherein the second soybean plant or second soybean germplasmcomprises an exotic soybean strain or an elite soybean strain.
 10. Themethod of claim 1, wherein the detecting comprises amplifying saidmarker loci and detecting the resulting amplified marker amplicon. 11.The method of claim 10, wherein the amplifying comprises: (a) admixingan amplification primer or amplification primer pair for each markerlocus being amplified with a nucleic acid isolated from the firstsoybean plant or the first soybean germplasm, wherein the primer orprimer pair is complementary or partially complementary to a variant orfragment of the genomic locus comprising the marker locus, and iscapable of initiating DNA polymerization by a DNA polymerase using thesoybean nucleic acid as a template; and b) extending the primer orprimer pair in a DNA polymerization reaction comprising a DNA polymeraseand a template nucleic acid to generate at least one amplicon.
 12. Themethod of claim 11, wherein said method comprises: amplifying a variantor fragment of one or more polynucleotides comprising SEQ ID NOs: 157 or158.
 13. The method of claim 11, wherein said primer or primer paircomprises: a variant or fragment of one or more polynucleotidescomprising SEQ ID NOs: 157, 158, or complements thereof.
 14. The methodof claim 13, wherein said primer or primer pair comprises: a nucleicacid sequence comprising SEQ ID NOs: 82, 83, 84, 85, 86, or variants orfragments thereof.
 15. The method of claim 14, wherein said primer paircomprises: SEQ ID NO: 82 and SEQ ID NO:
 83. 16. The method of claim 11,wherein the method further comprises providing one or more labelednucleic acid probes suitable for detection of each marker locus beingamplified.
 17. The method of claim 16, wherein said labeled nucleic acidprobe comprises: a nucleic acid sequence comprising a variant orfragment of one or more polynucleotides comprising SEQ ID NOs: 157, 158,or complements thereof.
 18. The method of claim 17, wherein the labelednucleic acid probe comprises: a nucleic acid sequence comprising SEQ IDNOs: 109 or
 110. 19. The method of claim 1, wherein the detectingcomprises DNA sequencing of said marker loci.
 20. An isolatedpolynucleotide capable of detecting a marker locus of the soybean genomecomprising: (a) S04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1,S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1, or amarker closely linked thereto; (b) S07162-1-Q1 or a marker closelylinked thereto; (c) S07161-1-Q1 or a marker closely linked thereto; (d)S00350-1-A, S02183-1-A, or a marker closely linked thereto; (e)S01519-1-A, S08177-1-Q1, S00479-1-A, S02136-1-A, S00875-1-A,S12875-1-Q1, S12950-1-Q1, S12947-1-Q1, S12933-1-Q1, S12853-1-Q1,S03246-1-A, S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, S02621-1-A, ora marker closely linked thereto; (f) S02874-1-A, S04785-1-A, or a markerclosely linked thereto; (g) S04348-1-A, S01209-1-A, S01999-1-A, or amarker closely linked thereto; (h) S04937-2-A, S04937-1-Q1, S04938-1-A,S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1, S06787-2-Q1,S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1, S06805-1-Q1,S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, S06792-1-Q1, or amarker closely linked thereto; (i) S03252-1-A, S02112-1-A, or a markerclosely linked thereto; or (j) S02074-1-A, S03991-1-A, or a markerclosely linked thereto.
 21. The isolated polynucleotide of claim 20,wherein the polynucleotide comprises: (a) a polynucleotide comprising:(i) SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70or 71; (ii) SEQ ID NOs: 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81; (iii)SEQ ID NOs: 82, 83, 84, 85 or 86; or (iv) SEQ ID NOs: 159, 160, 161,162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189,190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203,204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217,218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245,246, 247 or 248; (b) a polynucleotide comprising: (i) SEQ ID NOs: 87,88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,105 or 106; (ii) SEQ ID NOs: 107 or 108; (iii) SEQ ID NOs: 109 or 110;or (iv) SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258,259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300,301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314,315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328,329, 330, 331, 332, 333, 334, 335, 336, 337 or 338; (c) a polynucleotidehaving at least 90% sequence identity to the polynucleotides set forthin parts (a) or (b); or (d) a polynucleotide comprising at least 10contiguous nucleotides of the polynucleotides set forth in parts (a) or(b).
 22. A kit for detecting or selecting at least one soybean plant orsoybean germplasm with improved resistance to soybean cyst nematode, thekit comprising: a) primers or probes for detecting one or more markerloci associated with resistance to soybean cyst nematode, wherein theprimers or probes are capable of detecting a marker locus, wherein: (i)the marker locus is between about marker Sat_123 and about markerSatt453 on linkage group B1; (ii) the marker locus is between aboutmarker Sat_207 and about marker Satt713 on linkage group C1; (iii) themarker locus is between about marker Satt574 and about marker Satt615 onlinkage group D2; (iv) the marker locus is flanked by marker locusS00875 and S02621 on linkage group D1b; (v) the marker locus is flankedby marker locus S00479 and S02136 on linkage group D1b; (vi) the markerlocus is flanked by marker locus Sat_264 and BARC-020449-04623 onlinkage group B2; (vii) the marker locus is flanked by marker locusS02874 and S04785 on linkage group B2; (viii) the marker locus isflanked by marker locus S04348 and S01999 on linkage group B1; (ix) themarker locus is flanked by marker locus S01209 and S01999 on linkagegroup B1; (x) the marker locus is flanked by marker locus Satt557 andSatt307 on linkage group C2; (xi) the marker locus is flanked by markerlocus S03252 and S02112 on linkage group C2; (xii) the marker locuscomprises S00350-1-A, S02183-1-A, or a marker closely linked thereto; or(xiii) the marker locus is flanked by marker locus S02074 and S03991 onlinkage group L; and b) instructions for using the primers or probes fordetecting the one or more marker loci and correlating the detectedmarker loci with predicted resistance to soybean cyst nematode.
 23. Thekit of claim 22, wherein the primers or probes are capable of detectinga marker locus comprising (a) S04196-1-B, S04938-1-A, S04937-1-Q1,S08344-1-Q1, S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1,S04197-1, or a marker closely linked thereto; (b) S07162-1-Q1 or amarker closely linked thereto; (c) S07161-1-Q1 or a marker closelylinked thereto; (d) S01519-1-A, S08177-1-Q1, S00479-1-A, S02136-1-A,S00875-1-A, S12875-1-Q1, S12950-1-Q1, S12947-1-Q1, S12933-1-Q1,S12853-1-Q1, S03246-1-A, S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081,S02621-1-A, or a marker closely linked thereto; (e) S02874-1-A,S04785-1-A, or a marker closely linked thereto; (f) S04348-1-A,S01209-1-A, S01999-1-A, or a marker closely linked thereto; (g)S04937-2-A, S04937-1-Q1, S04938-1-A, S04938-2-A, S06786-2-Q1,S06786-3-Q1, S06786-1-Q1, S06787-2-Q1, S06787-1-Q1, S06803-1-Q1,S06804-1-Q1, S06788-1-Q1, S06805-1-Q1, S06789-1-Q1, S06790-1-Q1,S06791-2-Q1, S06791-1-Q1, S06792-1-Q1, or a marker closely linkedthereto; (h) S03252-1-A, S02112-1-A, or a marker closely linked thereto;or (i) S02074-1-A, S03991-1-A, or a marker closely linked thereto. 24.The method of claim 1, further comprising detecting in the genome ofsaid first soybean plant or in the genome of said first soybeangermplasm at least one or more marker locus that is associated with theresistance, wherein: (a) the at least one marker locus is between aboutmarker Sat_123 and about marker Satt453 on linkage group B1; (b) the atleast one marker locus is between about marker Sat_207 and about markerSatt713 on linkage group C1; (c) the at least one marker locus isbetween about marker Satt574 and about marker Satt615 on linkage groupD2; (d) the at least one marker locus is flanked by marker locus S00875and S02621 on linkage group D1b; (e) the at least one marker locus isflanked by marker locus S00479 and S02136 on linkage group D1b; (f) theat least one marker locus is flanked by marker locus Sat_264 andBARC-020449-04623 on linkage group B2; (g) the at least one marker locusis flanked by marker locus S02874 and S04785 on linkage group B2; (h)the at least one marker locus is flanked by marker locus S04348 andS01999 on linkage group B1; the at least one marker locus is flanked bymarker locus S01209 and S01999 on linkage group B1; the at least onemarker locus is flanked by marker locus Satt557 and Satt307 on linkagegroup C2; (k) the at least one marker locus is flanked by marker locusS03252 and S02112 on linkage group C2; (1) the at least one marker locuscomprises S00350-1-A, S02183-1-A, or a marker closely linked thereto; or(m) the at least one marker locus is flanked by marker locus S02074 andS03991 on linkage group L.